Loading the genome
The following was taken without modification from my earlier pyogenes analyses.
annotations = import.gff3("reference/genome/gas.gff", asRangedData=FALSE)
annotation_info = as.data.frame(annotations)
genes = annotation_info[annotation_info$type=="gene",]
rownames(genes) = genes$Note
genes$ID = genes$Note
gene_annotations = subset(genes, select = c("start", "end", "width", "strand", "Name", "protein_id", "ID"))
short_annotations = gene_annotations[,c("ID", "Name")]
short_annotations$spy = rownames(short_annotations)
colnames(short_annotations) = c("ID", "Name", "Spy")
write_xls(data=genes, sheet="genes", rowname="ID", file='simple_comparison.xls')
microbes = read.csv(file="reference/microbesonline/MGAS_5005_annotations.tab.gz", header=1, sep="\t")
microbes_go = microbes[,c("sysName","GO")]
go_entries = strsplit(as.character(microbes_go$GO), split=",", perl=TRUE)
microbes_go_oneperrow = data.frame(name = rep(microbes_go$sysName, sapply(go_entries, length)), GO = unlist(go_entries))
microbes_go = microbes_go_oneperrow
rm(microbes_go_oneperrow)
rm(go_entries)
## These are used for gene ontology stuff...
microbes_lengths = microbes[,c("sysName", "start","stop")]
microbes_lengths$length = abs(microbes$start - microbes$stop)
microbes_lengths = microbes_lengths[,c("sysName","length")]Generating tooltips
This block is used for cases when making clicky html graphs.
tooltip_data = genes
tooltip_data = tooltip_data[,c("ID","Name", "locus_tag")]
tooltip_data$tooltip = paste(tooltip_data$Name, tooltip_data$locus_tag, sep=": ")
tooltip_data$tooltip = gsub("\\+", " ", tooltip_data$tooltip)
rownames(tooltip_data) = tooltip_data$ID
tooltip_data = tooltip_data[-1]
tooltip_data = tooltip_data[-1]
tooltip_data = tooltip_data[-1]
head(tooltip_data)## tooltip
## M5005_Spy0001 dnaA: M5005_Spy_0001
## M5005_Spy0002 dnaN: M5005_Spy_0002
## M5005_Spy0003 M5005_Spy_0003: M5005_Spy_0003
## M5005_Spy0004 ychF: M5005_Spy_0004
## M5005_Spy0005 pth: M5005_Spy_0005
## M5005_Spy0006 trcF: M5005_Spy_0006Experimental design
I tried a few different alignment parameters. There is a separate experiment for each set of parameters so that if we wish, we can compare parameters.
all_mga_v0M1 = create_expt("all_samples.csv", suffix="_forward-trimmed-v0M1.count.xz", genes=genes, by_sample=TRUE, savefile="all_mga_v0M1")## [1] "This function needs the conditions and batches to be an explicit column in the sample sheet."
## [1] "Please note that thus function assumes a specific set of columns in the sample sheet:"
## [1] "The most important ones are: Sample.ID, Stage, Type."
## [1] "Other columns it will attempt to create by itself, but if"
## [1] "batch and condition are provided, that is a nice help."
## [1] "processed_data/count_tables/HPGL0406/hpgl0406_forward-trimmed-v0M1.count.xz contains 1931 rows."
## [1] "processed_data/count_tables/HPGL0407/hpgl0407_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0408/hpgl0408_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0409/hpgl0409_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0149/hpgl0149_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0150/hpgl0150_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0147/hpgl0147_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0148/hpgl0148_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0410/hpgl0410_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0411/hpgl0411_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0412/hpgl0412_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0413/hpgl0413_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0414/hpgl0414_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0416/hpgl0416_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0415/hpgl0415_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0417/hpgl0417_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0418/hpgl0418_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0419/hpgl0419_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0420/hpgl0420_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0421/hpgl0421_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0422/hpgl0422_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0423/hpgl0423_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0424/hpgl0424_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0425/hpgl0425_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0531/hpgl0531_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0531A/hpgl0531a_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0532/hpgl0532_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0532A/hpgl0532a_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0533/hpgl0533_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0533A/hpgl0533a_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0534/hpgl0534_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0534A/hpgl0534a_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0535/hpgl0535_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0535A/hpgl0535a_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0536/hpgl0536_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0536A/hpgl0536a_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0537/hpgl0537_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0537A/hpgl0537a_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0538/hpgl0538_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0538A/hpgl0538a_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0539/hpgl0539_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0539A/hpgl0539a_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0540/hpgl0540_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0540A/hpgl0540a_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0541/hpgl0541_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0541A/hpgl0541a_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0542/hpgl0542_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0542A/hpgl0542a_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0543/hpgl0543_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0544/hpgl0544_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0545/hpgl0545_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0546/hpgl0546_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0547/hpgl0547_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0548/hpgl0548_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0549/hpgl0549_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0550/hpgl0550_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0551/hpgl0551_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0552/hpgl0552_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0553/hpgl0553_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0554/hpgl0554_forward-trimmed-v0M1.count.xz contains 1931 rows and merges to 1931 rows."all_mga_v1M1l20 = create_expt("all_samples.csv", suffix="_forward-trimmed-v1M1l20.count.xz", genes=genes, by_sample=TRUE, savefile="all_mga_v1M1l20")## [1] "This function needs the conditions and batches to be an explicit column in the sample sheet."
## [1] "Please note that thus function assumes a specific set of columns in the sample sheet:"
## [1] "The most important ones are: Sample.ID, Stage, Type."
## [1] "Other columns it will attempt to create by itself, but if"
## [1] "batch and condition are provided, that is a nice help."
## [1] "processed_data/count_tables/HPGL0406/hpgl0406_forward-trimmed-v1M1l20.count.xz contains 1931 rows."
## [1] "processed_data/count_tables/HPGL0407/hpgl0407_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0408/hpgl0408_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0409/hpgl0409_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0149/hpgl0149_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0150/hpgl0150_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0147/hpgl0147_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0148/hpgl0148_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0410/hpgl0410_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0411/hpgl0411_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0412/hpgl0412_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0413/hpgl0413_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0414/hpgl0414_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0416/hpgl0416_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0415/hpgl0415_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0417/hpgl0417_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0418/hpgl0418_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0419/hpgl0419_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0420/hpgl0420_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0421/hpgl0421_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0422/hpgl0422_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0423/hpgl0423_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0424/hpgl0424_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0425/hpgl0425_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0531/hpgl0531_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0531A/hpgl0531a_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0532/hpgl0532_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0532A/hpgl0532a_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0533/hpgl0533_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0533A/hpgl0533a_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0534/hpgl0534_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0534A/hpgl0534a_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0535/hpgl0535_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0535A/hpgl0535a_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0536/hpgl0536_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0536A/hpgl0536a_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0537/hpgl0537_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0537A/hpgl0537a_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0538/hpgl0538_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0538A/hpgl0538a_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0539/hpgl0539_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0539A/hpgl0539a_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0540/hpgl0540_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0540A/hpgl0540a_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0541/hpgl0541_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0541A/hpgl0541a_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0542/hpgl0542_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0542A/hpgl0542a_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0543/hpgl0543_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0544/hpgl0544_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0545/hpgl0545_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0546/hpgl0546_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0547/hpgl0547_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0548/hpgl0548_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0549/hpgl0549_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0550/hpgl0550_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0551/hpgl0551_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0552/hpgl0552_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0553/hpgl0553_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0554/hpgl0554_forward-trimmed-v1M1l20.count.xz contains 1931 rows and merges to 1931 rows."all_mga_v2M1 = create_expt("all_samples.csv", suffix="_forward-trimmed-v2M1.count.xz", genes=genes, by_sample=TRUE, savefile="all_mga_v2M1")## [1] "This function needs the conditions and batches to be an explicit column in the sample sheet."
## [1] "Please note that thus function assumes a specific set of columns in the sample sheet:"
## [1] "The most important ones are: Sample.ID, Stage, Type."
## [1] "Other columns it will attempt to create by itself, but if"
## [1] "batch and condition are provided, that is a nice help."
## [1] "processed_data/count_tables/HPGL0406/hpgl0406_forward-trimmed-v2M1.count.xz contains 1931 rows."
## [1] "processed_data/count_tables/HPGL0407/hpgl0407_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0408/hpgl0408_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0409/hpgl0409_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0149/hpgl0149_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0150/hpgl0150_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0147/hpgl0147_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0148/hpgl0148_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0410/hpgl0410_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0411/hpgl0411_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0412/hpgl0412_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0413/hpgl0413_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0414/hpgl0414_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0416/hpgl0416_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0415/hpgl0415_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0417/hpgl0417_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0418/hpgl0418_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0419/hpgl0419_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0420/hpgl0420_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0421/hpgl0421_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0422/hpgl0422_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0423/hpgl0423_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0424/hpgl0424_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0425/hpgl0425_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0531/hpgl0531_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0531A/hpgl0531a_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0532/hpgl0532_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0532A/hpgl0532a_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0533/hpgl0533_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0533A/hpgl0533a_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0534/hpgl0534_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0534A/hpgl0534a_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0535/hpgl0535_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0535A/hpgl0535a_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0536/hpgl0536_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0536A/hpgl0536a_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0537/hpgl0537_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0537A/hpgl0537a_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0538/hpgl0538_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0538A/hpgl0538a_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0539/hpgl0539_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0539A/hpgl0539a_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0540/hpgl0540_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0540A/hpgl0540a_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0541/hpgl0541_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0541A/hpgl0541a_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0542/hpgl0542_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0542A/hpgl0542a_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0543/hpgl0543_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0544/hpgl0544_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0545/hpgl0545_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0546/hpgl0546_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0547/hpgl0547_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0548/hpgl0548_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0549/hpgl0549_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0550/hpgl0550_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0551/hpgl0551_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0552/hpgl0552_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0553/hpgl0553_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."
## [1] "processed_data/count_tables/HPGL0554/hpgl0554_forward-trimmed-v2M1.count.xz contains 1931 rows and merges to 1931 rows."Normalize data and perform initial metrics
The following block will print out so much information!
norm_v0M1 = normalize_expt(expt=all_mga_v0M1, norm="quant", convert="cpm", filter_low="cbcb", batch='sva', transform='log2')## [1] "This function will replace the expt$expressionset slot with the log2(quant(cpm))'d data."
## [1] "It saves the current data into a slot named: expt$backup_expressionset"
## [1] "It will also save copies of each step along the way in expt$normalized with the corresponding libsizes."
## [1] "Keep the libsizes in mind when invoking limma. The appropriate libsize is the non-log(cpm(normalized))."
## [1] "This is most likely kept in the slot called: 'new_expt$normalized$normalized_counts$libsize' which is copied into new_expt$best_libsize"
## [1] "Before batch correction, 8380 entries 0<x<1."
## Number of significant surrogate variables is: 3
## Iteration (out of 5 ):1 2 3 4 5 [1] "The number of elements which are < 0 after batch correction is: 2221"
## [1] "Found 2221 values equal to 0, adding 0.5 to the matrix."norm_v1M1l20 = normalize_expt(expt=all_mga_v1M1l20, transform="log2", norm="quant", convert="cpm", filter_low="cbcb")## [1] "This function will replace the expt$expressionset slot with the log2(quant(cpm))'d data."
## [1] "It saves the current data into a slot named: expt$backup_expressionset"
## [1] "It will also save copies of each step along the way in expt$normalized with the corresponding libsizes."
## [1] "Keep the libsizes in mind when invoking limma. The appropriate libsize is the non-log(cpm(normalized))."
## [1] "This is most likely kept in the slot called: 'new_expt$normalized$normalized_counts$libsize' which is copied into new_expt$best_libsize"
## [1] "Not correcting the count-data for batch effects. If batch is included in EdgerR/limma's model, then this is probably wise; but in extreme batch effects this is a good parameter to play with."normalized = normalize_expt(expt=all_mga_v2M1, transform="log2", norm="quant", convert="cpm", filter_low="cbcb")## [1] "This function will replace the expt$expressionset slot with the log2(quant(cpm))'d data."
## [1] "It saves the current data into a slot named: expt$backup_expressionset"
## [1] "It will also save copies of each step along the way in expt$normalized with the corresponding libsizes."
## [1] "Keep the libsizes in mind when invoking limma. The appropriate libsize is the non-log(cpm(normalized))."
## [1] "This is most likely kept in the slot called: 'new_expt$normalized$normalized_counts$libsize' which is copied into new_expt$best_libsize"
## [1] "Not correcting the count-data for batch effects. If batch is included in EdgerR/limma's model, then this is probably wise; but in extreme batch effects this is a good parameter to play with."tt = hpgl_pca(norm_v0M1)
tt$plot
many_raw_metrics = graph_metrics(all_mga_v0M1)## Graphing number of non-zero genes with respect to CPM by library.
## Graphing library sizes.
## Adding log10
## Graphing a boxplot on log scale.## [1] "I think this probably should be put on a log scale to be visible."## Graphing a correlation heatmap.
## Graphing a standard median correlation.
## Graphing a distance heatmap.
## Graphing a standard median distance.
## Graphing a PCA plot.
## Plotting a density plot.## [1] "Perhaps this data should be plotted on the log scale, add log=TRUE to try it out."## Using as id variables
many_norm_metrics = graph_metrics(normalized)## Graphing number of non-zero genes with respect to CPM by library.
## Graphing library sizes.
## Adding log10
## Graphing a boxplot on log scale.
## Graphing a correlation heatmap.
## Graphing a standard median correlation.
## Graphing a distance heatmap.
## Graphing a standard median distance.
## Graphing a PCA plot.
## Plotting a density plot.
summary(many_raw_metrics)## Length Class Mode
## nonzero 9 gg list
## libsize 9 gg list
## boxplot 9 gg list
## corheat 3 recordedplot list
## smc 3 recordedplot list
## disheat 3 recordedplot list
## smd 3 recordedplot list
## pcaplot 10 gg list
## pcatable 8 data.frame list
## pcares 4 data.frame list
## pcavar 59 -none- numeric
## density 9 gg list
## qq 0 -none- NULL
## ma 0 -none- NULLtiff(file="figures/libsize.tiff", res=90, width=8, height=8, units='in')
many_raw_metrics$libsize
dev.off()## X11cairo
## 2tiff(file="figures/raw_boxplot.tiff", res=90, width=8, height=8, units='in')
many_raw_metrics$boxplot + scale_y_log10()## Warning: Removed 6056 rows containing non-finite values (stat_boxplot).dev.off()## X11cairo
## 2tiff(file="figures/raw_density.tiff", res=90, width=8, height=8, units='in')
many_raw_metrics$density + scale_x_log10()## Warning: Removed 68 rows containing non-finite values (stat_density).## Warning: Removed 69 rows containing non-finite values (stat_density).## Warning: Removed 117 rows containing non-finite values (stat_density).## Warning: Removed 116 rows containing non-finite values (stat_density).## Warning: Removed 70 rows containing non-finite values (stat_density).## Warning: Removed 64 rows containing non-finite values (stat_density).## Warning: Removed 98 rows containing non-finite values (stat_density).## Warning: Removed 108 rows containing non-finite values (stat_density).## Warning: Removed 84 rows containing non-finite values (stat_density).## Warning: Removed 91 rows containing non-finite values (stat_density).## Warning: Removed 162 rows containing non-finite values (stat_density).## Warning: Removed 146 rows containing non-finite values (stat_density).## Warning: Removed 91 rows containing non-finite values (stat_density).## Warning: Removed 103 rows containing non-finite values (stat_density).## Warning: Removed 145 rows containing non-finite values (stat_density).## Warning: Removed 136 rows containing non-finite values (stat_density).## Warning: Removed 87 rows containing non-finite values (stat_density).## Warning: Removed 71 rows containing non-finite values (stat_density).## Warning: Removed 120 rows containing non-finite values (stat_density).## Warning: Removed 125 rows containing non-finite values (stat_density).## Warning: Removed 94 rows containing non-finite values (stat_density).## Warning: Removed 88 rows containing non-finite values (stat_density).## Warning: Removed 129 rows containing non-finite values (stat_density).## Warning: Removed 129 rows containing non-finite values (stat_density).## Warning: Removed 76 rows containing non-finite values (stat_density).## Warning: Removed 76 rows containing non-finite values (stat_density).## Warning: Removed 75 rows containing non-finite values (stat_density).## Warning: Removed 75 rows containing non-finite values (stat_density).## Warning: Removed 97 rows containing non-finite values (stat_density).## Warning: Removed 107 rows containing non-finite values (stat_density).## Warning: Removed 106 rows containing non-finite values (stat_density).## Warning: Removed 96 rows containing non-finite values (stat_density).## Warning: Removed 78 rows containing non-finite values (stat_density).## Warning: Removed 77 rows containing non-finite values (stat_density).## Warning: Removed 79 rows containing non-finite values (stat_density).## Warning: Removed 82 rows containing non-finite values (stat_density).## Warning: Removed 100 rows containing non-finite values (stat_density).## Warning: Removed 83 rows containing non-finite values (stat_density).## Warning: Removed 91 rows containing non-finite values (stat_density).## Warning: Removed 93 rows containing non-finite values (stat_density).## Warning: Removed 111 rows containing non-finite values (stat_density).## Warning: Removed 111 rows containing non-finite values (stat_density).## Warning: Removed 111 rows containing non-finite values (stat_density).## Warning: Removed 93 rows containing non-finite values (stat_density).## Warning: Removed 86 rows containing non-finite values (stat_density).## Warning: Removed 88 rows containing non-finite values (stat_density).## Warning: Removed 93 rows containing non-finite values (stat_density).## Warning: Removed 89 rows containing non-finite values (stat_density).## Warning: Removed 97 rows containing non-finite values (stat_density).## Warning: Removed 96 rows containing non-finite values (stat_density).## Warning: Removed 127 rows containing non-finite values (stat_density).## Warning: Removed 122 rows containing non-finite values (stat_density).## Warning: Removed 97 rows containing non-finite values (stat_density).## Warning: Removed 105 rows containing non-finite values (stat_density).## Warning: Removed 123 rows containing non-finite values (stat_density).## Warning: Removed 107 rows containing non-finite values (stat_density).## Warning: Removed 129 rows containing non-finite values (stat_density).## Warning: Removed 126 rows containing non-finite values (stat_density).## Warning: Removed 127 rows containing non-finite values (stat_density).## Warning: Removed 116 rows containing non-finite values (stat_density).dev.off()## X11cairo
## 2tiff(file="figures/norm_corheat.tiff", res=90, width=8, height=8, units='in')
many_norm_metrics$corheat
dev.off()## X11cairo
## 2tiff(file="figures/norm_smc.tiff", res=90, width=8, height=8, units='in')
many_norm_metrics$smc
dev.off()## X11cairo
## 2tiff(file="figures/norm_disheat.tiff", res=90, width=8, height=8, units='in')
many_norm_metrics$disheat
dev.off()## X11cairo
## 2tiff(file="figures/all_pca_norm.tiff", res=90, width=8, height=8, units='in')
all_pca = hpgl_pca(normalized, labels='')
all_pca$plot
dev.off()## X11cairo
## 2Splitting and analyzing data subsets
There are too many sample types/conditions/batches to do a comparison of them all. So I am splitting out a few relevant portions of the data and performing a simple pairwise comparison for each. In each instance, the data is being mapped onto the KEGG pathways.
Lots of subsets
thy_el_mutants = expt_subset(normalized, "condition=='mga1_el_thy'|condition=='mga2_el_thy'|condition=='mga3_el_thy'", by_definitions=TRUE)
thy_el_mga1 = expt_subset(normalized, "(condition=='wt_el_thy'&batch=='a')|condition=='mga1_el_thy'", by_definitions=TRUE)
thy_el_mga2 = expt_subset(normalized, "(condition=='wt_el_thy'&batch!='a')|condition=='mga2_el_thy'", by_definitions=TRUE)
thy_el_mga3 = expt_subset(normalized, "(batch!='a'&condition=='wt_el_thy')|condition=='mga3_el_thy'", by_definitions=TRUE)
thy_ll_mga1 = expt_subset(normalized, "(condition=='wt_ll_thy'&batch=='b')|condition=='mga1_ll_thy'", by_definitions=TRUE)
thy_ll_mga2 = expt_subset(normalized, "(condition=='wt_ll_thy'&batch!='b')|condition=='mga2_ll_thy'", by_definitions=TRUE)
thy_ll_mga3 = expt_subset(normalized, "(batch!='b'&condition=='wt_ll_thy')|condition=='mga3_ll_thy'", by_definitions=TRUE)
thy_st_mga1 = expt_subset(normalized, "batch=='a'&(condition=='wt_st_thy'|condition=='mga1_st_thy')", by_definitions=TRUE)
thy_st_mga2 = expt_subset(normalized, "batch=='d'&(condition=='wt_st_thy'|condition=='mga2_st_thy')", by_definitions=TRUE)
thy_st_mga3 = expt_subset(normalized, "batch=='d'&(condition=='wt_st_thy'|condition=='mga3_st_thy')", by_definitions=TRUE)
c_ll_mga1 = expt_subset(normalized, "(condition=='wt_ll_c'&batch=='a')|condition=='mga1_ll_c'", by_definitions=TRUE)
c_ll_mga2 = expt_subset(normalized, "batch!='a'&(condition=='wt_ll_c'|condition=='mga2_ll_c')", by_definitions=TRUE)
c_ll_mga3 = expt_subset(normalized, "batch!='a'&(condition=='wt_ll_c'|condition=='mga3_ll_c')", by_definitions=TRUE)
thyc_ll_wt = expt_subset(normalized, "(condition=='wt_ll_thy'|condition=='wt_ll_c')&(batch!='b')&(batch!='a')", by_definitions=TRUE)Some interesting pca plots
hpgl_pca(thy_el_mutants, labels=as.character(thy_el_mutants$design$mutantname))$plot
hpgl_pca(thy_el_mga2, labels=as.character(thy_el_mga2$design$mutantname))$plot
tiff(file="figures/thy_el_mga3_pca.tiff", width=8, height=8, units='in', res=90)
hpgl_pca(thy_el_mga3, labels=as.character(thy_el_mga3$design$mutantname))$plot
dev.off()## X11cairo
## 2hpgl_pca(thy_ll_mga2, labels=as.character(thy_ll_mga2$design$mutantname))$plot
hpgl_pca(thy_ll_mga3, labels=as.character(thy_ll_mga3$design$mutantname))$plot
hpgl_pca(thy_st_mga2, labels=as.character(thy_st_mga2$design$mutantname))$plot
hpgl_pca(thy_st_mga3, labels=as.character(thy_st_mga3$design$mutantname))$plot
hpgl_pca(c_ll_mga3, labels=as.character(c_ll_mga3$design$mutantname))$plot
hpgl_pca(thyc_ll_wt, labels=as.character(thyc_ll_wt$design$mutantname))$plot
hpgl_pca(c_ll_mga2, labels=as.character(c_ll_mga2$design$mutantname))$plot
Simple Comparisons
thy_el_comp1 = simple_comparison(thy_el_mga1, batch=FALSE, sheet="thy_el_comp1")## [1] "There is only one batch! I can only include condition in the model."## Warning in lmrob.S(x, y, control = control, mf = mf): S refinements did not
## converge (to refine.tol=1e-07) in 200 (= k.max) steps## Warning in lmrob.S(x, y, control = control, mf = mf): S refinements did not
## converge (to refine.tol=1e-07) in 200 (= k.max) steps## No binwidth nor bins provided, setting it to 0.0396500013301601 in order to have 500 bins.tiff(file="figures/thy_el_mga1_scatter.tiff", width=8, height=8, units='in', res=90)
thy_el_comp1$coefficient_scatter
dev.off()## X11cairo
## 2thy_el_comp2 = simple_comparison(thy_el_mga2, batch=FALSE, sheet="thy_el_comp2")## [1] "There is only one batch! I can only include condition in the model."## No binwidth nor bins provided, setting it to 0.0395568899082915 in order to have 500 bins.
tiff(file="figures/thy_el_mga2_scatter.tiff", width=8, height=8, units='in', res=90)
thy_el_comp2$coefficient_scatter
dev.off()## X11cairo
## 2thy_el_comp3 = simple_comparison(thy_el_mga3, batch=FALSE, sheet="thy_el_comp3")## [1] "There is only one batch! I can only include condition in the model."## No binwidth nor bins provided, setting it to 0.0395577190646362 in order to have 500 bins.tiff(file="figures/thy_el_mga3_scatter.tiff", width=8, height=8, units='in', res=90)
thy_el_comp3$coefficient_scatter
dev.off()## X11cairo
## 2thy_ll_comp1 = simple_comparison(thy_ll_mga1, batch=FALSE, sheet="thy_ll_comp1")## [1] "There is only one batch! I can only include condition in the model."## No binwidth nor bins provided, setting it to 0.0396973065438939 in order to have 500 bins.thy_ll_comp1$coefficient_scatter
thy_ll_comp2 = simple_comparison(thy_ll_mga2, batch=FALSE, sheet="thy_ll_comp2")## [1] "There is only one batch! I can only include condition in the model."## No binwidth nor bins provided, setting it to 0.0384047620191099 in order to have 500 bins.thy_ll_comp2$coefficient_scatter
thy_ll_comp3 = simple_comparison(thy_ll_mga3, batch=FALSE, sheet="thy_ll_comp3")## [1] "There is only one batch! I can only include condition in the model."## No binwidth nor bins provided, setting it to 0.039383453938633 in order to have 500 bins.thy_ll_comp3$coefficient_scatter
thy_st_comp1 = simple_comparison(thy_st_mga1, batch=FALSE, sheet="thy_st_comp1")## [1] "There is only one batch! I can only include condition in the model."## No binwidth nor bins provided, setting it to 0.0391171684988306 in order to have 500 bins.thy_st_comp1$coefficient_scatter
thy_st_comp2 = simple_comparison(thy_st_mga2, batch=FALSE, sheet="thy_st_comp2")## [1] "There is only one batch! I can only include condition in the model."## No binwidth nor bins provided, setting it to 0.0390557605904307 in order to have 500 bins.thy_st_comp2$coefficient_scatter
thy_st_comp3 = simple_comparison(thy_st_mga3, batch=FALSE, sheet="thy_st_comp3")## [1] "There is only one batch! I can only include condition in the model."## No binwidth nor bins provided, setting it to 0.0390559485053854 in order to have 500 bins.thy_st_comp3$coefficient_scatter
c_ll_comp1 = simple_comparison(c_ll_mga1, batch=FALSE, sheet="c_ll_comp1")## [1] "There is only one batch! I can only include condition in the model."## No binwidth nor bins provided, setting it to 0.0385759252840497 in order to have 500 bins.c_ll_comp1$coefficient_scatter
c_ll_comp2 = simple_comparison(c_ll_mga2, batch=FALSE, sheet="c_ll_comp2")## [1] "There is only one batch! I can only include condition in the model."## No binwidth nor bins provided, setting it to 0.0386259600580167 in order to have 500 bins.c_ll_comp2$coefficient_scatter
c_ll_comp3 = simple_comparison(c_ll_mga3, batch=FALSE, sheet="c_ll_comp3")## [1] "There is only one batch! I can only include condition in the model."## No binwidth nor bins provided, setting it to 0.0386259600580167 in order to have 500 bins.c_ll_comp3$coefficient_scatter
thyc_ll_comp = simple_comparison(thyc_ll_wt, batch=FALSE, sheet="thyc_ll_comp")## No binwidth nor bins provided, setting it to 0.0390028744398102 in order to have 500 bins.thyc_ll_comp$coefficient_scatter
#funk = thyc_ll_comp$table
#widths = data.frame(ID=rownames(genes), width=genes$width)
#simple_goseq(de_genes=funk, lengths=genes$width)
all_data = exprs(normalized$expressionset)
all_libsize = normalized$best_libsize
all_design = normalized$design
cond = as.factor(all_design$condition)
batch = as.factor(all_design$batch)
complete_model = model.matrix(~0 + cond + batch)New contrasts
## a (mut2/wt) / (mut3/wt) THY EL
## b (mut2/wt) / (mut3/wt) THY LL
## c (mut2/wt) / (mut3/wt) THY ST
## d (mut2/wt) / (mut3/wt) C LL
## e (b / d) ## Which is vvvv
## ((mut2/wt) / (mut3/wt) / (mut2/wt) / (mut3/wt))
## f ## Take the intersection of the final lists from b vs. d above
tmpnames = colnames(complete_model)
tmpnames = gsub("cond","", tmpnames)
colnames(complete_model) = tmpnames
complete_voom = hpgl_voom(all_data, complete_model, libsize=all_libsize, logged=normalized$transform, converted=normalized$convert)
complete_voom$plot
complete_fit = lmFit(complete_voom, complete_model)
all_contrasts = makeContrasts(
mga1_el_thy=mga1_el_thy,
mga1_ll_c=mga1_ll_c,
mga1_ll_cf=mga1_ll_cf,
mga1_ll_cg=mga1_ll_cg,
mga1_ll_thy=mga1_ll_thy,
mga1_st_thy=mga1_st_thy,
mga2_el_thy=mga2_el_thy,
mga2_ll_c=mga2_ll_c,
mga2_ll_thy=mga2_ll_thy,
mga2_st_thy=mga2_st_thy,
mga3_el_thy=mga3_el_thy,
mga3_ll_c=mga3_ll_c,
mga3_ll_thy=mga3_ll_thy,
mga3_st_thy=mga3_st_thy,
wt_el_thy=wt_el_thy,
wt_ll_c=wt_ll_c,
wt_ll_cf=wt_ll_cf,
wt_ll_cg=wt_ll_cg,
wt_ll_thy=wt_ll_thy,
wt_st_thy=wt_st_thy,
## Pairwise comparisons of interest
mga1wt_el_thy=(mga1_el_thy - wt_el_thy),
mga2wt_el_thy=(mga2_el_thy - wt_el_thy),
mga3wt_el_thy=(mga3_el_thy - wt_el_thy),
mga1wt_ll_thy=(mga1_ll_thy - wt_ll_thy),
mga2wt_ll_thy=(mga2_ll_thy - wt_ll_thy),
mga3wt_ll_thy=(mga3_ll_thy - wt_ll_thy),
mga1wt_st_thy=(mga1_st_thy - wt_st_thy),
mga2wt_st_thy=(mga2_st_thy - wt_st_thy),
mga3wt_st_thy=(mga3_st_thy - wt_st_thy),
mga1wt_ll_c=(mga1_ll_c - wt_ll_c),
mga2wt_ll_c=(mga2_ll_c - wt_ll_c),
mga3wt_ll_c=(mga3_ll_c - wt_ll_c),
wt_ll_cthy=(wt_ll_c - wt_ll_thy),
## Scenario 'a' from above (mut2/wt)/(mut3/wt)
## As written, the following 5 lines are pretty stupid and (using the first as an example)
## only perform: mga2_el_thy - mga3_el_thy.
##mga2mga3wt_el_thy=((mga2_el_thy - wt_el_thy) - (mga3_el_thy - wt_el_thy)),
##mga2mga3wt_ll_thy=((mga2_ll_thy - wt_ll_thy) - (mga3_ll_thy - wt_ll_thy)),
##mga2mga3wt_st_thy=((mga2_st_thy - wt_st_thy) - (mga3_st_thy - wt_st_thy)),
##mga2mga3wt_ll_c=((mga2_ll_c - wt_ll_c) - (mga3_ll_c - wt_ll_c)),
##mga2mga3wt_ll_cthy=(((mga2_ll_c - wt_ll_c)-(mga3_ll_c - wt_ll_c)) - ((mga2_ll_thy - wt_ll_thy)-(mga3_ll_thy - wt_ll_thy))),
levels=complete_voom$design)
all_fits = contrasts.fit(complete_fit, all_contrasts)
all_comparisons = eBayes(all_fits)
all_tables = topTable(all_comparisons, adjust="fdr", n=nrow(all_data))
## The above stuff can be replaced with:
my_contrasts = "mga1wt_el_thy=(mga1_el_thy - wt_el_thy),
mga2wt_el_thy=(mga2_el_thy - wt_el_thy),
mga3wt_el_thy=(mga3_el_thy - wt_el_thy),
mga1wt_ll_thy=(mga1_ll_thy - wt_ll_thy),
mga2wt_ll_thy=(mga2_ll_thy - wt_ll_thy),
mga3wt_ll_thy=(mga3_ll_thy - wt_ll_thy),
mga1wt_st_thy=(mga1_st_thy - wt_st_thy),
mga2wt_st_thy=(mga2_st_thy - wt_st_thy),
mga3wt_st_thy=(mga3_st_thy - wt_st_thy),
mga1wt_ll_c=(mga1_ll_c - wt_ll_c),
mga2wt_ll_c=(mga2_ll_c - wt_ll_c),
mga3wt_ll_c=(mga3_ll_c - wt_ll_c),
wt_ll_cthy=(wt_ll_c - wt_ll_thy),"
## mga2mga3wt_el_thy=((mga2_el_thy - wt_el_thy) - (mga3_el_thy - wt_el_thy)),
## mga2mga3wt_ll_thy=((mga2_ll_thy - wt_ll_thy) - (mga3_ll_thy - wt_ll_thy)),
## mga2mga3wt_st_thy=((mga2_st_thy - wt_st_thy) - (mga3_st_thy - wt_st_thy)),
## mga2mga3wt_ll_c=((mga2_ll_c - wt_ll_c) - (mga3_ll_c - wt_ll_c)),
## mga2mga3wt_ll_cthy=(((mga2_ll_c - wt_ll_c)-(mga3_ll_c - wt_ll_c)) - ((mga2_ll_thy - wt_ll_thy)-(mga3_ll_thy - wt_ll_thy))),"
crazytown = limma_pairwise(expt=normalized, conditions=cond, batches=batch, extra_contrasts=my_contrasts, libsize=all_libsize)## libsize was specified. This parameter has profound effects on limma's result.## [1] "As a reference, the identity is: mga1_el_thy = mga1_el_thy,"
## [1] "As a reference, the identity is: mga1_ll_c = mga1_ll_c,"
## [1] "As a reference, the identity is: mga1_ll_cf = mga1_ll_cf,"
## [1] "As a reference, the identity is: mga1_ll_cg = mga1_ll_cg,"
## [1] "As a reference, the identity is: mga1_ll_thy = mga1_ll_thy,"
## [1] "As a reference, the identity is: mga1_st_thy = mga1_st_thy,"
## [1] "As a reference, the identity is: mga2_el_thy = mga2_el_thy,"
## [1] "As a reference, the identity is: mga2_ll_c = mga2_ll_c,"
## [1] "As a reference, the identity is: mga2_ll_thy = mga2_ll_thy,"
## [1] "As a reference, the identity is: mga2_st_thy = mga2_st_thy,"
## [1] "As a reference, the identity is: mga3_el_thy = mga3_el_thy,"
## [1] "As a reference, the identity is: mga3_ll_c = mga3_ll_c,"
## [1] "As a reference, the identity is: mga3_ll_thy = mga3_ll_thy,"
## [1] "As a reference, the identity is: mga3_st_thy = mga3_st_thy,"
## [1] "As a reference, the identity is: wt_el_thy = wt_el_thy,"
## [1] "As a reference, the identity is: wt_ll_c = wt_ll_c,"
## [1] "As a reference, the identity is: wt_ll_cf = wt_ll_cf,"
## [1] "As a reference, the identity is: wt_ll_cg = wt_ll_cg,"
## [1] "As a reference, the identity is: wt_ll_thy = wt_ll_thy,"
## [1] "As a reference, the identity is: wt_st_thy = wt_st_thy,"## 1: Printing table: mga1_el_thy
## 2: Printing table: mga1_ll_c
## 3: Printing table: mga1_ll_cf
## 4: Printing table: mga1_ll_cg
## 5: Printing table: mga1_ll_thy
## 6: Printing table: mga1_st_thy
## 7: Printing table: mga2_el_thy
## 8: Printing table: mga2_ll_c
## 9: Printing table: mga2_ll_thy
## 10: Printing table: mga2_st_thy
## 11: Printing table: mga3_el_thy
## 12: Printing table: mga3_ll_c
## 13: Printing table: mga3_ll_thy
## 14: Printing table: mga3_st_thy
## 15: Printing table: wt_el_thy
## 16: Printing table: wt_ll_c
## 17: Printing table: wt_ll_cf
## 18: Printing table: wt_ll_cg
## 19: Printing table: wt_ll_thy
## 20: Printing table: wt_st_thy
## 21: Printing table: mga1_ll_c_minus_mga1_el_thy
## 22: Printing table: mga1_ll_cf_minus_mga1_el_thy
## 23: Printing table: mga1_ll_cg_minus_mga1_el_thy
## 24: Printing table: mga1_ll_thy_minus_mga1_el_thy
## 25: Printing table: mga1_st_thy_minus_mga1_el_thy
## 26: Printing table: mga2_el_thy_minus_mga1_el_thy
## 27: Printing table: mga2_ll_c_minus_mga1_el_thy
## 28: Printing table: mga2_ll_thy_minus_mga1_el_thy
## 29: Printing table: mga2_st_thy_minus_mga1_el_thy
## 30: Printing table: mga3_el_thy_minus_mga1_el_thy
## 31: Printing table: mga3_ll_c_minus_mga1_el_thy
## 32: Printing table: mga3_ll_thy_minus_mga1_el_thy
## 33: Printing table: mga3_st_thy_minus_mga1_el_thy
## 34: Printing table: wt_el_thy_minus_mga1_el_thy
## 35: Printing table: wt_ll_c_minus_mga1_el_thy
## 36: Printing table: wt_ll_cf_minus_mga1_el_thy
## 37: Printing table: wt_ll_cg_minus_mga1_el_thy
## 38: Printing table: wt_ll_thy_minus_mga1_el_thy
## 39: Printing table: wt_st_thy_minus_mga1_el_thy
## 40: Printing table: mga1_ll_cf_minus_mga1_ll_c
## 41: Printing table: mga1_ll_cg_minus_mga1_ll_c
## 42: Printing table: mga1_ll_thy_minus_mga1_ll_c
## 43: Printing table: mga1_st_thy_minus_mga1_ll_c
## 44: Printing table: mga2_el_thy_minus_mga1_ll_c
## 45: Printing table: mga2_ll_c_minus_mga1_ll_c
## 46: Printing table: mga2_ll_thy_minus_mga1_ll_c
## 47: Printing table: mga2_st_thy_minus_mga1_ll_c
## 48: Printing table: mga3_el_thy_minus_mga1_ll_c
## 49: Printing table: mga3_ll_c_minus_mga1_ll_c
## 50: Printing table: mga3_ll_thy_minus_mga1_ll_c
## 51: Printing table: mga3_st_thy_minus_mga1_ll_c
## 52: Printing table: wt_el_thy_minus_mga1_ll_c
## 53: Printing table: wt_ll_c_minus_mga1_ll_c
## 54: Printing table: wt_ll_cf_minus_mga1_ll_c
## 55: Printing table: wt_ll_cg_minus_mga1_ll_c
## 56: Printing table: wt_ll_thy_minus_mga1_ll_c
## 57: Printing table: wt_st_thy_minus_mga1_ll_c
## 58: Printing table: mga1_ll_cg_minus_mga1_ll_cf
## 59: Printing table: mga1_ll_thy_minus_mga1_ll_cf
## 60: Printing table: mga1_st_thy_minus_mga1_ll_cf
## 61: Printing table: mga2_el_thy_minus_mga1_ll_cf
## 62: Printing table: mga2_ll_c_minus_mga1_ll_cf
## 63: Printing table: mga2_ll_thy_minus_mga1_ll_cf
## 64: Printing table: mga2_st_thy_minus_mga1_ll_cf
## 65: Printing table: mga3_el_thy_minus_mga1_ll_cf
## 66: Printing table: mga3_ll_c_minus_mga1_ll_cf
## 67: Printing table: mga3_ll_thy_minus_mga1_ll_cf
## 68: Printing table: mga3_st_thy_minus_mga1_ll_cf
## 69: Printing table: wt_el_thy_minus_mga1_ll_cf
## 70: Printing table: wt_ll_c_minus_mga1_ll_cf
## 71: Printing table: wt_ll_cf_minus_mga1_ll_cf
## 72: Printing table: wt_ll_cg_minus_mga1_ll_cf
## 73: Printing table: wt_ll_thy_minus_mga1_ll_cf
## 74: Printing table: wt_st_thy_minus_mga1_ll_cf
## 75: Printing table: mga1_ll_thy_minus_mga1_ll_cg
## 76: Printing table: mga1_st_thy_minus_mga1_ll_cg
## 77: Printing table: mga2_el_thy_minus_mga1_ll_cg
## 78: Printing table: mga2_ll_c_minus_mga1_ll_cg
## 79: Printing table: mga2_ll_thy_minus_mga1_ll_cg
## 80: Printing table: mga2_st_thy_minus_mga1_ll_cg
## 81: Printing table: mga3_el_thy_minus_mga1_ll_cg
## 82: Printing table: mga3_ll_c_minus_mga1_ll_cg
## 83: Printing table: mga3_ll_thy_minus_mga1_ll_cg
## 84: Printing table: mga3_st_thy_minus_mga1_ll_cg
## 85: Printing table: wt_el_thy_minus_mga1_ll_cg
## 86: Printing table: wt_ll_c_minus_mga1_ll_cg
## 87: Printing table: wt_ll_cf_minus_mga1_ll_cg
## 88: Printing table: wt_ll_cg_minus_mga1_ll_cg
## 89: Printing table: wt_ll_thy_minus_mga1_ll_cg
## 90: Printing table: wt_st_thy_minus_mga1_ll_cg
## 91: Printing table: mga1_st_thy_minus_mga1_ll_thy
## 92: Printing table: mga2_el_thy_minus_mga1_ll_thy
## 93: Printing table: mga2_ll_c_minus_mga1_ll_thy
## 94: Printing table: mga2_ll_thy_minus_mga1_ll_thy
## 95: Printing table: mga2_st_thy_minus_mga1_ll_thy
## 96: Printing table: mga3_el_thy_minus_mga1_ll_thy
## 97: Printing table: mga3_ll_c_minus_mga1_ll_thy
## 98: Printing table: mga3_ll_thy_minus_mga1_ll_thy
## 99: Printing table: mga3_st_thy_minus_mga1_ll_thy
## 100: Printing table: wt_el_thy_minus_mga1_ll_thy
## 101: Printing table: wt_ll_c_minus_mga1_ll_thy
## 102: Printing table: wt_ll_cf_minus_mga1_ll_thy
## 103: Printing table: wt_ll_cg_minus_mga1_ll_thy
## 104: Printing table: wt_ll_thy_minus_mga1_ll_thy
## 105: Printing table: wt_st_thy_minus_mga1_ll_thy
## 106: Printing table: mga2_el_thy_minus_mga1_st_thy
## 107: Printing table: mga2_ll_c_minus_mga1_st_thy
## 108: Printing table: mga2_ll_thy_minus_mga1_st_thy
## 109: Printing table: mga2_st_thy_minus_mga1_st_thy
## 110: Printing table: mga3_el_thy_minus_mga1_st_thy
## 111: Printing table: mga3_ll_c_minus_mga1_st_thy
## 112: Printing table: mga3_ll_thy_minus_mga1_st_thy
## 113: Printing table: mga3_st_thy_minus_mga1_st_thy
## 114: Printing table: wt_el_thy_minus_mga1_st_thy
## 115: Printing table: wt_ll_c_minus_mga1_st_thy
## 116: Printing table: wt_ll_cf_minus_mga1_st_thy
## 117: Printing table: wt_ll_cg_minus_mga1_st_thy
## 118: Printing table: wt_ll_thy_minus_mga1_st_thy
## 119: Printing table: wt_st_thy_minus_mga1_st_thy
## 120: Printing table: mga2_ll_c_minus_mga2_el_thy
## 121: Printing table: mga2_ll_thy_minus_mga2_el_thy
## 122: Printing table: mga2_st_thy_minus_mga2_el_thy
## 123: Printing table: mga3_el_thy_minus_mga2_el_thy
## 124: Printing table: mga3_ll_c_minus_mga2_el_thy
## 125: Printing table: mga3_ll_thy_minus_mga2_el_thy
## 126: Printing table: mga3_st_thy_minus_mga2_el_thy
## 127: Printing table: wt_el_thy_minus_mga2_el_thy
## 128: Printing table: wt_ll_c_minus_mga2_el_thy
## 129: Printing table: wt_ll_cf_minus_mga2_el_thy
## 130: Printing table: wt_ll_cg_minus_mga2_el_thy
## 131: Printing table: wt_ll_thy_minus_mga2_el_thy
## 132: Printing table: wt_st_thy_minus_mga2_el_thy
## 133: Printing table: mga2_ll_thy_minus_mga2_ll_c
## 134: Printing table: mga2_st_thy_minus_mga2_ll_c
## 135: Printing table: mga3_el_thy_minus_mga2_ll_c
## 136: Printing table: mga3_ll_c_minus_mga2_ll_c
## 137: Printing table: mga3_ll_thy_minus_mga2_ll_c
## 138: Printing table: mga3_st_thy_minus_mga2_ll_c
## 139: Printing table: wt_el_thy_minus_mga2_ll_c
## 140: Printing table: wt_ll_c_minus_mga2_ll_c
## 141: Printing table: wt_ll_cf_minus_mga2_ll_c
## 142: Printing table: wt_ll_cg_minus_mga2_ll_c
## 143: Printing table: wt_ll_thy_minus_mga2_ll_c
## 144: Printing table: wt_st_thy_minus_mga2_ll_c
## 145: Printing table: mga2_st_thy_minus_mga2_ll_thy
## 146: Printing table: mga3_el_thy_minus_mga2_ll_thy
## 147: Printing table: mga3_ll_c_minus_mga2_ll_thy
## 148: Printing table: mga3_ll_thy_minus_mga2_ll_thy
## 149: Printing table: mga3_st_thy_minus_mga2_ll_thy
## 150: Printing table: wt_el_thy_minus_mga2_ll_thy
## 151: Printing table: wt_ll_c_minus_mga2_ll_thy
## 152: Printing table: wt_ll_cf_minus_mga2_ll_thy
## 153: Printing table: wt_ll_cg_minus_mga2_ll_thy
## 154: Printing table: wt_ll_thy_minus_mga2_ll_thy
## 155: Printing table: wt_st_thy_minus_mga2_ll_thy
## 156: Printing table: mga3_el_thy_minus_mga2_st_thy
## 157: Printing table: mga3_ll_c_minus_mga2_st_thy
## 158: Printing table: mga3_ll_thy_minus_mga2_st_thy
## 159: Printing table: mga3_st_thy_minus_mga2_st_thy
## 160: Printing table: wt_el_thy_minus_mga2_st_thy
## 161: Printing table: wt_ll_c_minus_mga2_st_thy
## 162: Printing table: wt_ll_cf_minus_mga2_st_thy
## 163: Printing table: wt_ll_cg_minus_mga2_st_thy
## 164: Printing table: wt_ll_thy_minus_mga2_st_thy
## 165: Printing table: wt_st_thy_minus_mga2_st_thy
## 166: Printing table: mga3_ll_c_minus_mga3_el_thy
## 167: Printing table: mga3_ll_thy_minus_mga3_el_thy
## 168: Printing table: mga3_st_thy_minus_mga3_el_thy
## 169: Printing table: wt_el_thy_minus_mga3_el_thy
## 170: Printing table: wt_ll_c_minus_mga3_el_thy
## 171: Printing table: wt_ll_cf_minus_mga3_el_thy
## 172: Printing table: wt_ll_cg_minus_mga3_el_thy
## 173: Printing table: wt_ll_thy_minus_mga3_el_thy
## 174: Printing table: wt_st_thy_minus_mga3_el_thy
## 175: Printing table: mga3_ll_thy_minus_mga3_ll_c
## 176: Printing table: mga3_st_thy_minus_mga3_ll_c
## 177: Printing table: wt_el_thy_minus_mga3_ll_c
## 178: Printing table: wt_ll_c_minus_mga3_ll_c
## 179: Printing table: wt_ll_cf_minus_mga3_ll_c
## 180: Printing table: wt_ll_cg_minus_mga3_ll_c
## 181: Printing table: wt_ll_thy_minus_mga3_ll_c
## 182: Printing table: wt_st_thy_minus_mga3_ll_c
## 183: Printing table: mga3_st_thy_minus_mga3_ll_thy
## 184: Printing table: wt_el_thy_minus_mga3_ll_thy
## 185: Printing table: wt_ll_c_minus_mga3_ll_thy
## 186: Printing table: wt_ll_cf_minus_mga3_ll_thy
## 187: Printing table: wt_ll_cg_minus_mga3_ll_thy
## 188: Printing table: wt_ll_thy_minus_mga3_ll_thy
## 189: Printing table: wt_st_thy_minus_mga3_ll_thy
## 190: Printing table: wt_el_thy_minus_mga3_st_thy
## 191: Printing table: wt_ll_c_minus_mga3_st_thy
## 192: Printing table: wt_ll_cf_minus_mga3_st_thy
## 193: Printing table: wt_ll_cg_minus_mga3_st_thy
## 194: Printing table: wt_ll_thy_minus_mga3_st_thy
## 195: Printing table: wt_st_thy_minus_mga3_st_thy
## 196: Printing table: wt_ll_c_minus_wt_el_thy
## 197: Printing table: wt_ll_cf_minus_wt_el_thy
## 198: Printing table: wt_ll_cg_minus_wt_el_thy
## 199: Printing table: wt_ll_thy_minus_wt_el_thy
## 200: Printing table: wt_st_thy_minus_wt_el_thy
## 201: Printing table: wt_ll_cf_minus_wt_ll_c
## 202: Printing table: wt_ll_cg_minus_wt_ll_c
## 203: Printing table: wt_ll_thy_minus_wt_ll_c
## 204: Printing table: wt_st_thy_minus_wt_ll_c
## 205: Printing table: wt_ll_cg_minus_wt_ll_cf
## 206: Printing table: wt_ll_thy_minus_wt_ll_cf
## 207: Printing table: wt_st_thy_minus_wt_ll_cf
## 208: Printing table: wt_ll_thy_minus_wt_ll_cg
## 209: Printing table: wt_st_thy_minus_wt_ll_cg
## 210: Printing table: wt_st_thy_minus_wt_ll_thy
## 211: Printing table: mga1wt_el_thy
## 212: Printing table: mga2wt_el_thy
## 213: Printing table: mga3wt_el_thy
## 214: Printing table: mga1wt_ll_thy
## 215: Printing table: mga2wt_ll_thy
## 216: Printing table: mga3wt_ll_thy
## 217: Printing table: mga1wt_st_thy
## 218: Printing table: mga2wt_st_thy
## 219: Printing table: mga3wt_st_thy
## 220: Printing table: mga1wt_ll_c
## 221: Printing table: mga2wt_ll_c
## 222: Printing table: mga3wt_ll_c
## 223: Printing table: wt_ll_cthylimma_results = crazytown$all_tables
supercrazytown = all_pairwise(expt=normalized, conditions=cond, batches=batch, extra_contrasts=my_contrasts)## libsize was not specified, this parameter has profound effects on limma's result.
## Using the libsize from expt$best_libsize.## [1] "As a reference, the identity is: mga1_el_thy = mga1_el_thy,"
## [1] "As a reference, the identity is: mga1_ll_c = mga1_ll_c,"
## [1] "As a reference, the identity is: mga1_ll_cf = mga1_ll_cf,"
## [1] "As a reference, the identity is: mga1_ll_cg = mga1_ll_cg,"
## [1] "As a reference, the identity is: mga1_ll_thy = mga1_ll_thy,"
## [1] "As a reference, the identity is: mga1_st_thy = mga1_st_thy,"
## [1] "As a reference, the identity is: mga2_el_thy = mga2_el_thy,"
## [1] "As a reference, the identity is: mga2_ll_c = mga2_ll_c,"
## [1] "As a reference, the identity is: mga2_ll_thy = mga2_ll_thy,"
## [1] "As a reference, the identity is: mga2_st_thy = mga2_st_thy,"
## [1] "As a reference, the identity is: mga3_el_thy = mga3_el_thy,"
## [1] "As a reference, the identity is: mga3_ll_c = mga3_ll_c,"
## [1] "As a reference, the identity is: mga3_ll_thy = mga3_ll_thy,"
## [1] "As a reference, the identity is: mga3_st_thy = mga3_st_thy,"
## [1] "As a reference, the identity is: wt_el_thy = wt_el_thy,"
## [1] "As a reference, the identity is: wt_ll_c = wt_ll_c,"
## [1] "As a reference, the identity is: wt_ll_cf = wt_ll_cf,"
## [1] "As a reference, the identity is: wt_ll_cg = wt_ll_cg,"
## [1] "As a reference, the identity is: wt_ll_thy = wt_ll_thy,"
## [1] "As a reference, the identity is: wt_st_thy = wt_st_thy,"## 1: Printing table: mga1_el_thy
## 2: Printing table: mga1_ll_c
## 3: Printing table: mga1_ll_cf
## 4: Printing table: mga1_ll_cg
## 5: Printing table: mga1_ll_thy
## 6: Printing table: mga1_st_thy
## 7: Printing table: mga2_el_thy
## 8: Printing table: mga2_ll_c
## 9: Printing table: mga2_ll_thy
## 10: Printing table: mga2_st_thy
## 11: Printing table: mga3_el_thy
## 12: Printing table: mga3_ll_c
## 13: Printing table: mga3_ll_thy
## 14: Printing table: mga3_st_thy
## 15: Printing table: wt_el_thy
## 16: Printing table: wt_ll_c
## 17: Printing table: wt_ll_cf
## 18: Printing table: wt_ll_cg
## 19: Printing table: wt_ll_thy
## 20: Printing table: wt_st_thy
## 21: Printing table: mga1_ll_c_minus_mga1_el_thy
## 22: Printing table: mga1_ll_cf_minus_mga1_el_thy
## 23: Printing table: mga1_ll_cg_minus_mga1_el_thy
## 24: Printing table: mga1_ll_thy_minus_mga1_el_thy
## 25: Printing table: mga1_st_thy_minus_mga1_el_thy
## 26: Printing table: mga2_el_thy_minus_mga1_el_thy
## 27: Printing table: mga2_ll_c_minus_mga1_el_thy
## 28: Printing table: mga2_ll_thy_minus_mga1_el_thy
## 29: Printing table: mga2_st_thy_minus_mga1_el_thy
## 30: Printing table: mga3_el_thy_minus_mga1_el_thy
## 31: Printing table: mga3_ll_c_minus_mga1_el_thy
## 32: Printing table: mga3_ll_thy_minus_mga1_el_thy
## 33: Printing table: mga3_st_thy_minus_mga1_el_thy
## 34: Printing table: wt_el_thy_minus_mga1_el_thy
## 35: Printing table: wt_ll_c_minus_mga1_el_thy
## 36: Printing table: wt_ll_cf_minus_mga1_el_thy
## 37: Printing table: wt_ll_cg_minus_mga1_el_thy
## 38: Printing table: wt_ll_thy_minus_mga1_el_thy
## 39: Printing table: wt_st_thy_minus_mga1_el_thy
## 40: Printing table: mga1_ll_cf_minus_mga1_ll_c
## 41: Printing table: mga1_ll_cg_minus_mga1_ll_c
## 42: Printing table: mga1_ll_thy_minus_mga1_ll_c
## 43: Printing table: mga1_st_thy_minus_mga1_ll_c
## 44: Printing table: mga2_el_thy_minus_mga1_ll_c
## 45: Printing table: mga2_ll_c_minus_mga1_ll_c
## 46: Printing table: mga2_ll_thy_minus_mga1_ll_c
## 47: Printing table: mga2_st_thy_minus_mga1_ll_c
## 48: Printing table: mga3_el_thy_minus_mga1_ll_c
## 49: Printing table: mga3_ll_c_minus_mga1_ll_c
## 50: Printing table: mga3_ll_thy_minus_mga1_ll_c
## 51: Printing table: mga3_st_thy_minus_mga1_ll_c
## 52: Printing table: wt_el_thy_minus_mga1_ll_c
## 53: Printing table: wt_ll_c_minus_mga1_ll_c
## 54: Printing table: wt_ll_cf_minus_mga1_ll_c
## 55: Printing table: wt_ll_cg_minus_mga1_ll_c
## 56: Printing table: wt_ll_thy_minus_mga1_ll_c
## 57: Printing table: wt_st_thy_minus_mga1_ll_c
## 58: Printing table: mga1_ll_cg_minus_mga1_ll_cf
## 59: Printing table: mga1_ll_thy_minus_mga1_ll_cf
## 60: Printing table: mga1_st_thy_minus_mga1_ll_cf
## 61: Printing table: mga2_el_thy_minus_mga1_ll_cf
## 62: Printing table: mga2_ll_c_minus_mga1_ll_cf
## 63: Printing table: mga2_ll_thy_minus_mga1_ll_cf
## 64: Printing table: mga2_st_thy_minus_mga1_ll_cf
## 65: Printing table: mga3_el_thy_minus_mga1_ll_cf
## 66: Printing table: mga3_ll_c_minus_mga1_ll_cf
## 67: Printing table: mga3_ll_thy_minus_mga1_ll_cf
## 68: Printing table: mga3_st_thy_minus_mga1_ll_cf
## 69: Printing table: wt_el_thy_minus_mga1_ll_cf
## 70: Printing table: wt_ll_c_minus_mga1_ll_cf
## 71: Printing table: wt_ll_cf_minus_mga1_ll_cf
## 72: Printing table: wt_ll_cg_minus_mga1_ll_cf
## 73: Printing table: wt_ll_thy_minus_mga1_ll_cf
## 74: Printing table: wt_st_thy_minus_mga1_ll_cf
## 75: Printing table: mga1_ll_thy_minus_mga1_ll_cg
## 76: Printing table: mga1_st_thy_minus_mga1_ll_cg
## 77: Printing table: mga2_el_thy_minus_mga1_ll_cg
## 78: Printing table: mga2_ll_c_minus_mga1_ll_cg
## 79: Printing table: mga2_ll_thy_minus_mga1_ll_cg
## 80: Printing table: mga2_st_thy_minus_mga1_ll_cg
## 81: Printing table: mga3_el_thy_minus_mga1_ll_cg
## 82: Printing table: mga3_ll_c_minus_mga1_ll_cg
## 83: Printing table: mga3_ll_thy_minus_mga1_ll_cg
## 84: Printing table: mga3_st_thy_minus_mga1_ll_cg
## 85: Printing table: wt_el_thy_minus_mga1_ll_cg
## 86: Printing table: wt_ll_c_minus_mga1_ll_cg
## 87: Printing table: wt_ll_cf_minus_mga1_ll_cg
## 88: Printing table: wt_ll_cg_minus_mga1_ll_cg
## 89: Printing table: wt_ll_thy_minus_mga1_ll_cg
## 90: Printing table: wt_st_thy_minus_mga1_ll_cg
## 91: Printing table: mga1_st_thy_minus_mga1_ll_thy
## 92: Printing table: mga2_el_thy_minus_mga1_ll_thy
## 93: Printing table: mga2_ll_c_minus_mga1_ll_thy
## 94: Printing table: mga2_ll_thy_minus_mga1_ll_thy
## 95: Printing table: mga2_st_thy_minus_mga1_ll_thy
## 96: Printing table: mga3_el_thy_minus_mga1_ll_thy
## 97: Printing table: mga3_ll_c_minus_mga1_ll_thy
## 98: Printing table: mga3_ll_thy_minus_mga1_ll_thy
## 99: Printing table: mga3_st_thy_minus_mga1_ll_thy
## 100: Printing table: wt_el_thy_minus_mga1_ll_thy
## 101: Printing table: wt_ll_c_minus_mga1_ll_thy
## 102: Printing table: wt_ll_cf_minus_mga1_ll_thy
## 103: Printing table: wt_ll_cg_minus_mga1_ll_thy
## 104: Printing table: wt_ll_thy_minus_mga1_ll_thy
## 105: Printing table: wt_st_thy_minus_mga1_ll_thy
## 106: Printing table: mga2_el_thy_minus_mga1_st_thy
## 107: Printing table: mga2_ll_c_minus_mga1_st_thy
## 108: Printing table: mga2_ll_thy_minus_mga1_st_thy
## 109: Printing table: mga2_st_thy_minus_mga1_st_thy
## 110: Printing table: mga3_el_thy_minus_mga1_st_thy
## 111: Printing table: mga3_ll_c_minus_mga1_st_thy
## 112: Printing table: mga3_ll_thy_minus_mga1_st_thy
## 113: Printing table: mga3_st_thy_minus_mga1_st_thy
## 114: Printing table: wt_el_thy_minus_mga1_st_thy
## 115: Printing table: wt_ll_c_minus_mga1_st_thy
## 116: Printing table: wt_ll_cf_minus_mga1_st_thy
## 117: Printing table: wt_ll_cg_minus_mga1_st_thy
## 118: Printing table: wt_ll_thy_minus_mga1_st_thy
## 119: Printing table: wt_st_thy_minus_mga1_st_thy
## 120: Printing table: mga2_ll_c_minus_mga2_el_thy
## 121: Printing table: mga2_ll_thy_minus_mga2_el_thy
## 122: Printing table: mga2_st_thy_minus_mga2_el_thy
## 123: Printing table: mga3_el_thy_minus_mga2_el_thy
## 124: Printing table: mga3_ll_c_minus_mga2_el_thy
## 125: Printing table: mga3_ll_thy_minus_mga2_el_thy
## 126: Printing table: mga3_st_thy_minus_mga2_el_thy
## 127: Printing table: wt_el_thy_minus_mga2_el_thy
## 128: Printing table: wt_ll_c_minus_mga2_el_thy
## 129: Printing table: wt_ll_cf_minus_mga2_el_thy
## 130: Printing table: wt_ll_cg_minus_mga2_el_thy
## 131: Printing table: wt_ll_thy_minus_mga2_el_thy
## 132: Printing table: wt_st_thy_minus_mga2_el_thy
## 133: Printing table: mga2_ll_thy_minus_mga2_ll_c
## 134: Printing table: mga2_st_thy_minus_mga2_ll_c
## 135: Printing table: mga3_el_thy_minus_mga2_ll_c
## 136: Printing table: mga3_ll_c_minus_mga2_ll_c
## 137: Printing table: mga3_ll_thy_minus_mga2_ll_c
## 138: Printing table: mga3_st_thy_minus_mga2_ll_c
## 139: Printing table: wt_el_thy_minus_mga2_ll_c
## 140: Printing table: wt_ll_c_minus_mga2_ll_c
## 141: Printing table: wt_ll_cf_minus_mga2_ll_c
## 142: Printing table: wt_ll_cg_minus_mga2_ll_c
## 143: Printing table: wt_ll_thy_minus_mga2_ll_c
## 144: Printing table: wt_st_thy_minus_mga2_ll_c
## 145: Printing table: mga2_st_thy_minus_mga2_ll_thy
## 146: Printing table: mga3_el_thy_minus_mga2_ll_thy
## 147: Printing table: mga3_ll_c_minus_mga2_ll_thy
## 148: Printing table: mga3_ll_thy_minus_mga2_ll_thy
## 149: Printing table: mga3_st_thy_minus_mga2_ll_thy
## 150: Printing table: wt_el_thy_minus_mga2_ll_thy
## 151: Printing table: wt_ll_c_minus_mga2_ll_thy
## 152: Printing table: wt_ll_cf_minus_mga2_ll_thy
## 153: Printing table: wt_ll_cg_minus_mga2_ll_thy
## 154: Printing table: wt_ll_thy_minus_mga2_ll_thy
## 155: Printing table: wt_st_thy_minus_mga2_ll_thy
## 156: Printing table: mga3_el_thy_minus_mga2_st_thy
## 157: Printing table: mga3_ll_c_minus_mga2_st_thy
## 158: Printing table: mga3_ll_thy_minus_mga2_st_thy
## 159: Printing table: mga3_st_thy_minus_mga2_st_thy
## 160: Printing table: wt_el_thy_minus_mga2_st_thy
## 161: Printing table: wt_ll_c_minus_mga2_st_thy
## 162: Printing table: wt_ll_cf_minus_mga2_st_thy
## 163: Printing table: wt_ll_cg_minus_mga2_st_thy
## 164: Printing table: wt_ll_thy_minus_mga2_st_thy
## 165: Printing table: wt_st_thy_minus_mga2_st_thy
## 166: Printing table: mga3_ll_c_minus_mga3_el_thy
## 167: Printing table: mga3_ll_thy_minus_mga3_el_thy
## 168: Printing table: mga3_st_thy_minus_mga3_el_thy
## 169: Printing table: wt_el_thy_minus_mga3_el_thy
## 170: Printing table: wt_ll_c_minus_mga3_el_thy
## 171: Printing table: wt_ll_cf_minus_mga3_el_thy
## 172: Printing table: wt_ll_cg_minus_mga3_el_thy
## 173: Printing table: wt_ll_thy_minus_mga3_el_thy
## 174: Printing table: wt_st_thy_minus_mga3_el_thy
## 175: Printing table: mga3_ll_thy_minus_mga3_ll_c
## 176: Printing table: mga3_st_thy_minus_mga3_ll_c
## 177: Printing table: wt_el_thy_minus_mga3_ll_c
## 178: Printing table: wt_ll_c_minus_mga3_ll_c
## 179: Printing table: wt_ll_cf_minus_mga3_ll_c
## 180: Printing table: wt_ll_cg_minus_mga3_ll_c
## 181: Printing table: wt_ll_thy_minus_mga3_ll_c
## 182: Printing table: wt_st_thy_minus_mga3_ll_c
## 183: Printing table: mga3_st_thy_minus_mga3_ll_thy
## 184: Printing table: wt_el_thy_minus_mga3_ll_thy
## 185: Printing table: wt_ll_c_minus_mga3_ll_thy
## 186: Printing table: wt_ll_cf_minus_mga3_ll_thy
## 187: Printing table: wt_ll_cg_minus_mga3_ll_thy
## 188: Printing table: wt_ll_thy_minus_mga3_ll_thy
## 189: Printing table: wt_st_thy_minus_mga3_ll_thy
## 190: Printing table: wt_el_thy_minus_mga3_st_thy
## 191: Printing table: wt_ll_c_minus_mga3_st_thy
## 192: Printing table: wt_ll_cf_minus_mga3_st_thy
## 193: Printing table: wt_ll_cg_minus_mga3_st_thy
## 194: Printing table: wt_ll_thy_minus_mga3_st_thy
## 195: Printing table: wt_st_thy_minus_mga3_st_thy
## 196: Printing table: wt_ll_c_minus_wt_el_thy
## 197: Printing table: wt_ll_cf_minus_wt_el_thy
## 198: Printing table: wt_ll_cg_minus_wt_el_thy
## 199: Printing table: wt_ll_thy_minus_wt_el_thy
## 200: Printing table: wt_st_thy_minus_wt_el_thy
## 201: Printing table: wt_ll_cf_minus_wt_ll_c
## 202: Printing table: wt_ll_cg_minus_wt_ll_c
## 203: Printing table: wt_ll_thy_minus_wt_ll_c
## 204: Printing table: wt_st_thy_minus_wt_ll_c
## 205: Printing table: wt_ll_cg_minus_wt_ll_cf
## 206: Printing table: wt_ll_thy_minus_wt_ll_cf
## 207: Printing table: wt_st_thy_minus_wt_ll_cf
## 208: Printing table: wt_ll_thy_minus_wt_ll_cg
## 209: Printing table: wt_st_thy_minus_wt_ll_cg
## 210: Printing table: wt_st_thy_minus_wt_ll_thy
## 211: Printing table: mga1wt_el_thy
## 212: Printing table: mga2wt_el_thy
## 213: Printing table: mga3wt_el_thy
## 214: Printing table: mga1wt_ll_thy
## 215: Printing table: mga2wt_ll_thy
## 216: Printing table: mga3wt_ll_thy
## 217: Printing table: mga1wt_st_thy
## 218: Printing table: mga2wt_st_thy
## 219: Printing table: mga3wt_st_thy
## 220: Printing table: mga1wt_ll_c
## 221: Printing table: mga2wt_ll_c
## 222: Printing table: mga3wt_ll_c
## 223: Printing table: wt_ll_cthy
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## At this time, this only does conditional models.
## Using EdgeR to normalize the data.
## Estimating the common dispersion.
## Estimating dispersion across genes.
## Estimating GLM Common dispersion.
## Estimating GLM Trended dispersion.
## Estimating GLM Tagged dispersion.## [1] "As a reference, the identity is: mga1_el_thy = mga1_el_thy,"
## [1] "As a reference, the identity is: mga1_ll_c = mga1_ll_c,"
## [1] "As a reference, the identity is: mga1_ll_cf = mga1_ll_cf,"
## [1] "As a reference, the identity is: mga1_ll_cg = mga1_ll_cg,"
## [1] "As a reference, the identity is: mga1_ll_thy = mga1_ll_thy,"
## [1] "As a reference, the identity is: mga1_st_thy = mga1_st_thy,"
## [1] "As a reference, the identity is: mga2_el_thy = mga2_el_thy,"
## [1] "As a reference, the identity is: mga2_ll_c = mga2_ll_c,"
## [1] "As a reference, the identity is: mga2_ll_thy = mga2_ll_thy,"
## [1] "As a reference, the identity is: mga2_st_thy = mga2_st_thy,"
## [1] "As a reference, the identity is: mga3_el_thy = mga3_el_thy,"
## [1] "As a reference, the identity is: mga3_ll_c = mga3_ll_c,"
## [1] "As a reference, the identity is: mga3_ll_thy = mga3_ll_thy,"
## [1] "As a reference, the identity is: mga3_st_thy = mga3_st_thy,"
## [1] "As a reference, the identity is: wt_el_thy = wt_el_thy,"
## [1] "As a reference, the identity is: wt_ll_c = wt_ll_c,"
## [1] "As a reference, the identity is: wt_ll_cf = wt_ll_cf,"
## [1] "As a reference, the identity is: wt_ll_cg = wt_ll_cg,"
## [1] "As a reference, the identity is: wt_ll_thy = wt_ll_thy,"
## [1] "As a reference, the identity is: wt_st_thy = wt_st_thy,"## 1: Performing mga1_ll_c_minus_mga1_el_thy contrast.
## 2: Performing mga1_ll_cf_minus_mga1_el_thy contrast.
## 3: Performing mga1_ll_cg_minus_mga1_el_thy contrast.
## 4: Performing mga1_ll_thy_minus_mga1_el_thy contrast.
## 5: Performing mga1_st_thy_minus_mga1_el_thy contrast.
## 6: Performing mga2_el_thy_minus_mga1_el_thy contrast.
## 7: Performing mga2_ll_c_minus_mga1_el_thy contrast.
## 8: Performing mga2_ll_thy_minus_mga1_el_thy contrast.
## 9: Performing mga2_st_thy_minus_mga1_el_thy contrast.
## 10: Performing mga3_el_thy_minus_mga1_el_thy contrast.
## 11: Performing mga3_ll_c_minus_mga1_el_thy contrast.
## 12: Performing mga3_ll_thy_minus_mga1_el_thy contrast.
## 13: Performing mga3_st_thy_minus_mga1_el_thy contrast.
## 14: Performing wt_el_thy_minus_mga1_el_thy contrast.
## 15: Performing wt_ll_c_minus_mga1_el_thy contrast.
## 16: Performing wt_ll_cf_minus_mga1_el_thy contrast.
## 17: Performing wt_ll_cg_minus_mga1_el_thy contrast.
## 18: Performing wt_ll_thy_minus_mga1_el_thy contrast.
## 19: Performing wt_st_thy_minus_mga1_el_thy contrast.
## 20: Performing mga1_ll_cf_minus_mga1_ll_c contrast.
## 21: Performing mga1_ll_cg_minus_mga1_ll_c contrast.
## 22: Performing mga1_ll_thy_minus_mga1_ll_c contrast.
## 23: Performing mga1_st_thy_minus_mga1_ll_c contrast.
## 24: Performing mga2_el_thy_minus_mga1_ll_c contrast.
## 25: Performing mga2_ll_c_minus_mga1_ll_c contrast.
## 26: Performing mga2_ll_thy_minus_mga1_ll_c contrast.
## 27: Performing mga2_st_thy_minus_mga1_ll_c contrast.
## 28: Performing mga3_el_thy_minus_mga1_ll_c contrast.
## 29: Performing mga3_ll_c_minus_mga1_ll_c contrast.
## 30: Performing mga3_ll_thy_minus_mga1_ll_c contrast.
## 31: Performing mga3_st_thy_minus_mga1_ll_c contrast.
## 32: Performing wt_el_thy_minus_mga1_ll_c contrast.
## 33: Performing wt_ll_c_minus_mga1_ll_c contrast.
## 34: Performing wt_ll_cf_minus_mga1_ll_c contrast.
## 35: Performing wt_ll_cg_minus_mga1_ll_c contrast.
## 36: Performing wt_ll_thy_minus_mga1_ll_c contrast.
## 37: Performing wt_st_thy_minus_mga1_ll_c contrast.
## 38: Performing mga1_ll_cg_minus_mga1_ll_cf contrast.
## 39: Performing mga1_ll_thy_minus_mga1_ll_cf contrast.
## 40: Performing mga1_st_thy_minus_mga1_ll_cf contrast.
## 41: Performing mga2_el_thy_minus_mga1_ll_cf contrast.
## 42: Performing mga2_ll_c_minus_mga1_ll_cf contrast.
## 43: Performing mga2_ll_thy_minus_mga1_ll_cf contrast.
## 44: Performing mga2_st_thy_minus_mga1_ll_cf contrast.
## 45: Performing mga3_el_thy_minus_mga1_ll_cf contrast.
## 46: Performing mga3_ll_c_minus_mga1_ll_cf contrast.
## 47: Performing mga3_ll_thy_minus_mga1_ll_cf contrast.
## 48: Performing mga3_st_thy_minus_mga1_ll_cf contrast.
## 49: Performing wt_el_thy_minus_mga1_ll_cf contrast.
## 50: Performing wt_ll_c_minus_mga1_ll_cf contrast.
## 51: Performing wt_ll_cf_minus_mga1_ll_cf contrast.
## 52: Performing wt_ll_cg_minus_mga1_ll_cf contrast.
## 53: Performing wt_ll_thy_minus_mga1_ll_cf contrast.
## 54: Performing wt_st_thy_minus_mga1_ll_cf contrast.
## 55: Performing mga1_ll_thy_minus_mga1_ll_cg contrast.
## 56: Performing mga1_st_thy_minus_mga1_ll_cg contrast.
## 57: Performing mga2_el_thy_minus_mga1_ll_cg contrast.
## 58: Performing mga2_ll_c_minus_mga1_ll_cg contrast.
## 59: Performing mga2_ll_thy_minus_mga1_ll_cg contrast.
## 60: Performing mga2_st_thy_minus_mga1_ll_cg contrast.
## 61: Performing mga3_el_thy_minus_mga1_ll_cg contrast.
## 62: Performing mga3_ll_c_minus_mga1_ll_cg contrast.
## 63: Performing mga3_ll_thy_minus_mga1_ll_cg contrast.
## 64: Performing mga3_st_thy_minus_mga1_ll_cg contrast.
## 65: Performing wt_el_thy_minus_mga1_ll_cg contrast.
## 66: Performing wt_ll_c_minus_mga1_ll_cg contrast.
## 67: Performing wt_ll_cf_minus_mga1_ll_cg contrast.
## 68: Performing wt_ll_cg_minus_mga1_ll_cg contrast.
## 69: Performing wt_ll_thy_minus_mga1_ll_cg contrast.
## 70: Performing wt_st_thy_minus_mga1_ll_cg contrast.
## 71: Performing mga1_st_thy_minus_mga1_ll_thy contrast.
## 72: Performing mga2_el_thy_minus_mga1_ll_thy contrast.
## 73: Performing mga2_ll_c_minus_mga1_ll_thy contrast.
## 74: Performing mga2_ll_thy_minus_mga1_ll_thy contrast.
## 75: Performing mga2_st_thy_minus_mga1_ll_thy contrast.
## 76: Performing mga3_el_thy_minus_mga1_ll_thy contrast.
## 77: Performing mga3_ll_c_minus_mga1_ll_thy contrast.
## 78: Performing mga3_ll_thy_minus_mga1_ll_thy contrast.
## 79: Performing mga3_st_thy_minus_mga1_ll_thy contrast.
## 80: Performing wt_el_thy_minus_mga1_ll_thy contrast.
## 81: Performing wt_ll_c_minus_mga1_ll_thy contrast.
## 82: Performing wt_ll_cf_minus_mga1_ll_thy contrast.
## 83: Performing wt_ll_cg_minus_mga1_ll_thy contrast.
## 84: Performing wt_ll_thy_minus_mga1_ll_thy contrast.
## 85: Performing wt_st_thy_minus_mga1_ll_thy contrast.
## 86: Performing mga2_el_thy_minus_mga1_st_thy contrast.
## 87: Performing mga2_ll_c_minus_mga1_st_thy contrast.
## 88: Performing mga2_ll_thy_minus_mga1_st_thy contrast.
## 89: Performing mga2_st_thy_minus_mga1_st_thy contrast.
## 90: Performing mga3_el_thy_minus_mga1_st_thy contrast.
## 91: Performing mga3_ll_c_minus_mga1_st_thy contrast.
## 92: Performing mga3_ll_thy_minus_mga1_st_thy contrast.
## 93: Performing mga3_st_thy_minus_mga1_st_thy contrast.
## 94: Performing wt_el_thy_minus_mga1_st_thy contrast.
## 95: Performing wt_ll_c_minus_mga1_st_thy contrast.
## 96: Performing wt_ll_cf_minus_mga1_st_thy contrast.
## 97: Performing wt_ll_cg_minus_mga1_st_thy contrast.
## 98: Performing wt_ll_thy_minus_mga1_st_thy contrast.
## 99: Performing wt_st_thy_minus_mga1_st_thy contrast.
## 100: Performing mga2_ll_c_minus_mga2_el_thy contrast.
## 101: Performing mga2_ll_thy_minus_mga2_el_thy contrast.
## 102: Performing mga2_st_thy_minus_mga2_el_thy contrast.
## 103: Performing mga3_el_thy_minus_mga2_el_thy contrast.
## 104: Performing mga3_ll_c_minus_mga2_el_thy contrast.
## 105: Performing mga3_ll_thy_minus_mga2_el_thy contrast.
## 106: Performing mga3_st_thy_minus_mga2_el_thy contrast.
## 107: Performing wt_el_thy_minus_mga2_el_thy contrast.
## 108: Performing wt_ll_c_minus_mga2_el_thy contrast.
## 109: Performing wt_ll_cf_minus_mga2_el_thy contrast.
## 110: Performing wt_ll_cg_minus_mga2_el_thy contrast.
## 111: Performing wt_ll_thy_minus_mga2_el_thy contrast.
## 112: Performing wt_st_thy_minus_mga2_el_thy contrast.
## 113: Performing mga2_ll_thy_minus_mga2_ll_c contrast.
## 114: Performing mga2_st_thy_minus_mga2_ll_c contrast.
## 115: Performing mga3_el_thy_minus_mga2_ll_c contrast.
## 116: Performing mga3_ll_c_minus_mga2_ll_c contrast.
## 117: Performing mga3_ll_thy_minus_mga2_ll_c contrast.
## 118: Performing mga3_st_thy_minus_mga2_ll_c contrast.
## 119: Performing wt_el_thy_minus_mga2_ll_c contrast.
## 120: Performing wt_ll_c_minus_mga2_ll_c contrast.
## 121: Performing wt_ll_cf_minus_mga2_ll_c contrast.
## 122: Performing wt_ll_cg_minus_mga2_ll_c contrast.
## 123: Performing wt_ll_thy_minus_mga2_ll_c contrast.
## 124: Performing wt_st_thy_minus_mga2_ll_c contrast.
## 125: Performing mga2_st_thy_minus_mga2_ll_thy contrast.
## 126: Performing mga3_el_thy_minus_mga2_ll_thy contrast.
## 127: Performing mga3_ll_c_minus_mga2_ll_thy contrast.
## 128: Performing mga3_ll_thy_minus_mga2_ll_thy contrast.
## 129: Performing mga3_st_thy_minus_mga2_ll_thy contrast.
## 130: Performing wt_el_thy_minus_mga2_ll_thy contrast.
## 131: Performing wt_ll_c_minus_mga2_ll_thy contrast.
## 132: Performing wt_ll_cf_minus_mga2_ll_thy contrast.
## 133: Performing wt_ll_cg_minus_mga2_ll_thy contrast.
## 134: Performing wt_ll_thy_minus_mga2_ll_thy contrast.
## 135: Performing wt_st_thy_minus_mga2_ll_thy contrast.
## 136: Performing mga3_el_thy_minus_mga2_st_thy contrast.
## 137: Performing mga3_ll_c_minus_mga2_st_thy contrast.
## 138: Performing mga3_ll_thy_minus_mga2_st_thy contrast.
## 139: Performing mga3_st_thy_minus_mga2_st_thy contrast.
## 140: Performing wt_el_thy_minus_mga2_st_thy contrast.
## 141: Performing wt_ll_c_minus_mga2_st_thy contrast.
## 142: Performing wt_ll_cf_minus_mga2_st_thy contrast.
## 143: Performing wt_ll_cg_minus_mga2_st_thy contrast.
## 144: Performing wt_ll_thy_minus_mga2_st_thy contrast.
## 145: Performing wt_st_thy_minus_mga2_st_thy contrast.
## 146: Performing mga3_ll_c_minus_mga3_el_thy contrast.
## 147: Performing mga3_ll_thy_minus_mga3_el_thy contrast.
## 148: Performing mga3_st_thy_minus_mga3_el_thy contrast.
## 149: Performing wt_el_thy_minus_mga3_el_thy contrast.
## 150: Performing wt_ll_c_minus_mga3_el_thy contrast.
## 151: Performing wt_ll_cf_minus_mga3_el_thy contrast.
## 152: Performing wt_ll_cg_minus_mga3_el_thy contrast.
## 153: Performing wt_ll_thy_minus_mga3_el_thy contrast.
## 154: Performing wt_st_thy_minus_mga3_el_thy contrast.
## 155: Performing mga3_ll_thy_minus_mga3_ll_c contrast.
## 156: Performing mga3_st_thy_minus_mga3_ll_c contrast.
## 157: Performing wt_el_thy_minus_mga3_ll_c contrast.
## 158: Performing wt_ll_c_minus_mga3_ll_c contrast.
## 159: Performing wt_ll_cf_minus_mga3_ll_c contrast.
## 160: Performing wt_ll_cg_minus_mga3_ll_c contrast.
## 161: Performing wt_ll_thy_minus_mga3_ll_c contrast.
## 162: Performing wt_st_thy_minus_mga3_ll_c contrast.
## 163: Performing mga3_st_thy_minus_mga3_ll_thy contrast.
## 164: Performing wt_el_thy_minus_mga3_ll_thy contrast.
## 165: Performing wt_ll_c_minus_mga3_ll_thy contrast.
## 166: Performing wt_ll_cf_minus_mga3_ll_thy contrast.
## 167: Performing wt_ll_cg_minus_mga3_ll_thy contrast.
## 168: Performing wt_ll_thy_minus_mga3_ll_thy contrast.
## 169: Performing wt_st_thy_minus_mga3_ll_thy contrast.
## 170: Performing wt_el_thy_minus_mga3_st_thy contrast.
## 171: Performing wt_ll_c_minus_mga3_st_thy contrast.
## 172: Performing wt_ll_cf_minus_mga3_st_thy contrast.
## 173: Performing wt_ll_cg_minus_mga3_st_thy contrast.
## 174: Performing wt_ll_thy_minus_mga3_st_thy contrast.
## 175: Performing wt_st_thy_minus_mga3_st_thy contrast.
## 176: Performing wt_ll_c_minus_wt_el_thy contrast.
## 177: Performing wt_ll_cf_minus_wt_el_thy contrast.
## 178: Performing wt_ll_cg_minus_wt_el_thy contrast.
## 179: Performing wt_ll_thy_minus_wt_el_thy contrast.
## 180: Performing wt_st_thy_minus_wt_el_thy contrast.
## 181: Performing wt_ll_cf_minus_wt_ll_c contrast.
## 182: Performing wt_ll_cg_minus_wt_ll_c contrast.
## 183: Performing wt_ll_thy_minus_wt_ll_c contrast.
## 184: Performing wt_st_thy_minus_wt_ll_c contrast.
## 185: Performing wt_ll_cg_minus_wt_ll_cf contrast.
## 186: Performing wt_ll_thy_minus_wt_ll_cf contrast.
## 187: Performing wt_st_thy_minus_wt_ll_cf contrast.
## 188: Performing wt_ll_thy_minus_wt_ll_cg contrast.
## 189: Performing wt_st_thy_minus_wt_ll_cg contrast.
## 190: Performing wt_st_thy_minus_wt_ll_thy contrast.
## 1/190: Comparing analyses for: mga1_ll_c_minus_mga1_el_thy
## 2/190: Comparing analyses for: mga1_ll_cf_minus_mga1_el_thy
## 3/190: Comparing analyses for: mga1_ll_cg_minus_mga1_el_thy
## 4/190: Comparing analyses for: mga1_ll_thy_minus_mga1_el_thy
## 5/190: Comparing analyses for: mga1_st_thy_minus_mga1_el_thy
## 6/190: Comparing analyses for: mga2_el_thy_minus_mga1_el_thy
## 7/190: Comparing analyses for: mga2_ll_c_minus_mga1_el_thy
## 8/190: Comparing analyses for: mga2_ll_thy_minus_mga1_el_thy
## 9/190: Comparing analyses for: mga2_st_thy_minus_mga1_el_thy
## 10/190: Comparing analyses for: mga3_el_thy_minus_mga1_el_thy
## 11/190: Comparing analyses for: mga3_ll_c_minus_mga1_el_thy
## 12/190: Comparing analyses for: mga3_ll_thy_minus_mga1_el_thy
## 13/190: Comparing analyses for: mga3_st_thy_minus_mga1_el_thy
## 14/190: Comparing analyses for: wt_el_thy_minus_mga1_el_thy
## 15/190: Comparing analyses for: wt_ll_c_minus_mga1_el_thy
## 16/190: Comparing analyses for: wt_ll_cf_minus_mga1_el_thy
## 17/190: Comparing analyses for: wt_ll_cg_minus_mga1_el_thy
## 18/190: Comparing analyses for: wt_ll_thy_minus_mga1_el_thy
## 19/190: Comparing analyses for: wt_st_thy_minus_mga1_el_thy
## 20/190: Comparing analyses for: mga1_ll_cf_minus_mga1_ll_c
## 21/190: Comparing analyses for: mga1_ll_cg_minus_mga1_ll_c
## 22/190: Comparing analyses for: mga1_ll_thy_minus_mga1_ll_c
## 23/190: Comparing analyses for: mga1_st_thy_minus_mga1_ll_c
## 24/190: Comparing analyses for: mga2_el_thy_minus_mga1_ll_c
## 25/190: Comparing analyses for: mga2_ll_c_minus_mga1_ll_c
## 26/190: Comparing analyses for: mga2_ll_thy_minus_mga1_ll_c
## 27/190: Comparing analyses for: mga2_st_thy_minus_mga1_ll_c
## 28/190: Comparing analyses for: mga3_el_thy_minus_mga1_ll_c
## 29/190: Comparing analyses for: mga3_ll_c_minus_mga1_ll_c
## 30/190: Comparing analyses for: mga3_ll_thy_minus_mga1_ll_c
## 31/190: Comparing analyses for: mga3_st_thy_minus_mga1_ll_c
## 32/190: Comparing analyses for: wt_el_thy_minus_mga1_ll_c
## 33/190: Comparing analyses for: wt_ll_c_minus_mga1_ll_c
## 34/190: Comparing analyses for: wt_ll_cf_minus_mga1_ll_c
## 35/190: Comparing analyses for: wt_ll_cg_minus_mga1_ll_c
## 36/190: Comparing analyses for: wt_ll_thy_minus_mga1_ll_c
## 37/190: Comparing analyses for: wt_st_thy_minus_mga1_ll_c
## 38/190: Comparing analyses for: mga1_ll_cg_minus_mga1_ll_cf
## 39/190: Comparing analyses for: mga1_ll_thy_minus_mga1_ll_cf
## 40/190: Comparing analyses for: mga1_st_thy_minus_mga1_ll_cf
## 41/190: Comparing analyses for: mga2_el_thy_minus_mga1_ll_cf
## 42/190: Comparing analyses for: mga2_ll_c_minus_mga1_ll_cf
## 43/190: Comparing analyses for: mga2_ll_thy_minus_mga1_ll_cf
## 44/190: Comparing analyses for: mga2_st_thy_minus_mga1_ll_cf
## 45/190: Comparing analyses for: mga3_el_thy_minus_mga1_ll_cf
## 46/190: Comparing analyses for: mga3_ll_c_minus_mga1_ll_cf
## 47/190: Comparing analyses for: mga3_ll_thy_minus_mga1_ll_cf
## 48/190: Comparing analyses for: mga3_st_thy_minus_mga1_ll_cf
## 49/190: Comparing analyses for: wt_el_thy_minus_mga1_ll_cf
## 50/190: Comparing analyses for: wt_ll_c_minus_mga1_ll_cf
## 51/190: Comparing analyses for: wt_ll_cf_minus_mga1_ll_cf
## 52/190: Comparing analyses for: wt_ll_cg_minus_mga1_ll_cf
## 53/190: Comparing analyses for: wt_ll_thy_minus_mga1_ll_cf
## 54/190: Comparing analyses for: wt_st_thy_minus_mga1_ll_cf
## 55/190: Comparing analyses for: mga1_ll_thy_minus_mga1_ll_cg
## 56/190: Comparing analyses for: mga1_st_thy_minus_mga1_ll_cg
## 57/190: Comparing analyses for: mga2_el_thy_minus_mga1_ll_cg
## 58/190: Comparing analyses for: mga2_ll_c_minus_mga1_ll_cg
## 59/190: Comparing analyses for: mga2_ll_thy_minus_mga1_ll_cg
## 60/190: Comparing analyses for: mga2_st_thy_minus_mga1_ll_cg
## 61/190: Comparing analyses for: mga3_el_thy_minus_mga1_ll_cg
## 62/190: Comparing analyses for: mga3_ll_c_minus_mga1_ll_cg
## 63/190: Comparing analyses for: mga3_ll_thy_minus_mga1_ll_cg
## 64/190: Comparing analyses for: mga3_st_thy_minus_mga1_ll_cg
## 65/190: Comparing analyses for: wt_el_thy_minus_mga1_ll_cg
## 66/190: Comparing analyses for: wt_ll_c_minus_mga1_ll_cg
## 67/190: Comparing analyses for: wt_ll_cf_minus_mga1_ll_cg
## 68/190: Comparing analyses for: wt_ll_cg_minus_mga1_ll_cg
## 69/190: Comparing analyses for: wt_ll_thy_minus_mga1_ll_cg
## 70/190: Comparing analyses for: wt_st_thy_minus_mga1_ll_cg
## 71/190: Comparing analyses for: mga1_st_thy_minus_mga1_ll_thy
## 72/190: Comparing analyses for: mga2_el_thy_minus_mga1_ll_thy
## 73/190: Comparing analyses for: mga2_ll_c_minus_mga1_ll_thy
## 74/190: Comparing analyses for: mga2_ll_thy_minus_mga1_ll_thy
## 75/190: Comparing analyses for: mga2_st_thy_minus_mga1_ll_thy
## 76/190: Comparing analyses for: mga3_el_thy_minus_mga1_ll_thy
## 77/190: Comparing analyses for: mga3_ll_c_minus_mga1_ll_thy
## 78/190: Comparing analyses for: mga3_ll_thy_minus_mga1_ll_thy
## 79/190: Comparing analyses for: mga3_st_thy_minus_mga1_ll_thy
## 80/190: Comparing analyses for: wt_el_thy_minus_mga1_ll_thy
## 81/190: Comparing analyses for: wt_ll_c_minus_mga1_ll_thy
## 82/190: Comparing analyses for: wt_ll_cf_minus_mga1_ll_thy
## 83/190: Comparing analyses for: wt_ll_cg_minus_mga1_ll_thy
## 84/190: Comparing analyses for: wt_ll_thy_minus_mga1_ll_thy
## 85/190: Comparing analyses for: wt_st_thy_minus_mga1_ll_thy
## 86/190: Comparing analyses for: mga2_el_thy_minus_mga1_st_thy
## 87/190: Comparing analyses for: mga2_ll_c_minus_mga1_st_thy
## 88/190: Comparing analyses for: mga2_ll_thy_minus_mga1_st_thy
## 89/190: Comparing analyses for: mga2_st_thy_minus_mga1_st_thy
## 90/190: Comparing analyses for: mga3_el_thy_minus_mga1_st_thy
## 91/190: Comparing analyses for: mga3_ll_c_minus_mga1_st_thy
## 92/190: Comparing analyses for: mga3_ll_thy_minus_mga1_st_thy
## 93/190: Comparing analyses for: mga3_st_thy_minus_mga1_st_thy
## 94/190: Comparing analyses for: wt_el_thy_minus_mga1_st_thy
## 95/190: Comparing analyses for: wt_ll_c_minus_mga1_st_thy
## 96/190: Comparing analyses for: wt_ll_cf_minus_mga1_st_thy
## 97/190: Comparing analyses for: wt_ll_cg_minus_mga1_st_thy
## 98/190: Comparing analyses for: wt_ll_thy_minus_mga1_st_thy
## 99/190: Comparing analyses for: wt_st_thy_minus_mga1_st_thy
## 100/190: Comparing analyses for: mga2_ll_c_minus_mga2_el_thy
## 101/190: Comparing analyses for: mga2_ll_thy_minus_mga2_el_thy
## 102/190: Comparing analyses for: mga2_st_thy_minus_mga2_el_thy
## 103/190: Comparing analyses for: mga3_el_thy_minus_mga2_el_thy
## 104/190: Comparing analyses for: mga3_ll_c_minus_mga2_el_thy
## 105/190: Comparing analyses for: mga3_ll_thy_minus_mga2_el_thy
## 106/190: Comparing analyses for: mga3_st_thy_minus_mga2_el_thy
## 107/190: Comparing analyses for: wt_el_thy_minus_mga2_el_thy
## 108/190: Comparing analyses for: wt_ll_c_minus_mga2_el_thy
## 109/190: Comparing analyses for: wt_ll_cf_minus_mga2_el_thy
## 110/190: Comparing analyses for: wt_ll_cg_minus_mga2_el_thy
## 111/190: Comparing analyses for: wt_ll_thy_minus_mga2_el_thy
## 112/190: Comparing analyses for: wt_st_thy_minus_mga2_el_thy
## 113/190: Comparing analyses for: mga2_ll_thy_minus_mga2_ll_c
## 114/190: Comparing analyses for: mga2_st_thy_minus_mga2_ll_c
## 115/190: Comparing analyses for: mga3_el_thy_minus_mga2_ll_c
## 116/190: Comparing analyses for: mga3_ll_c_minus_mga2_ll_c
## 117/190: Comparing analyses for: mga3_ll_thy_minus_mga2_ll_c
## 118/190: Comparing analyses for: mga3_st_thy_minus_mga2_ll_c
## 119/190: Comparing analyses for: wt_el_thy_minus_mga2_ll_c
## 120/190: Comparing analyses for: wt_ll_c_minus_mga2_ll_c
## 121/190: Comparing analyses for: wt_ll_cf_minus_mga2_ll_c
## 122/190: Comparing analyses for: wt_ll_cg_minus_mga2_ll_c
## 123/190: Comparing analyses for: wt_ll_thy_minus_mga2_ll_c
## 124/190: Comparing analyses for: wt_st_thy_minus_mga2_ll_c
## 125/190: Comparing analyses for: mga2_st_thy_minus_mga2_ll_thy
## 126/190: Comparing analyses for: mga3_el_thy_minus_mga2_ll_thy
## 127/190: Comparing analyses for: mga3_ll_c_minus_mga2_ll_thy
## 128/190: Comparing analyses for: mga3_ll_thy_minus_mga2_ll_thy
## 129/190: Comparing analyses for: mga3_st_thy_minus_mga2_ll_thy
## 130/190: Comparing analyses for: wt_el_thy_minus_mga2_ll_thy
## 131/190: Comparing analyses for: wt_ll_c_minus_mga2_ll_thy
## 132/190: Comparing analyses for: wt_ll_cf_minus_mga2_ll_thy
## 133/190: Comparing analyses for: wt_ll_cg_minus_mga2_ll_thy
## 134/190: Comparing analyses for: wt_ll_thy_minus_mga2_ll_thy
## 135/190: Comparing analyses for: wt_st_thy_minus_mga2_ll_thy
## 136/190: Comparing analyses for: mga3_el_thy_minus_mga2_st_thy
## 137/190: Comparing analyses for: mga3_ll_c_minus_mga2_st_thy
## 138/190: Comparing analyses for: mga3_ll_thy_minus_mga2_st_thy
## 139/190: Comparing analyses for: mga3_st_thy_minus_mga2_st_thy
## 140/190: Comparing analyses for: wt_el_thy_minus_mga2_st_thy
## 141/190: Comparing analyses for: wt_ll_c_minus_mga2_st_thy
## 142/190: Comparing analyses for: wt_ll_cf_minus_mga2_st_thy
## 143/190: Comparing analyses for: wt_ll_cg_minus_mga2_st_thy
## 144/190: Comparing analyses for: wt_ll_thy_minus_mga2_st_thy
## 145/190: Comparing analyses for: wt_st_thy_minus_mga2_st_thy
## 146/190: Comparing analyses for: mga3_ll_c_minus_mga3_el_thy
## 147/190: Comparing analyses for: mga3_ll_thy_minus_mga3_el_thy
## 148/190: Comparing analyses for: mga3_st_thy_minus_mga3_el_thy
## 149/190: Comparing analyses for: wt_el_thy_minus_mga3_el_thy
## 150/190: Comparing analyses for: wt_ll_c_minus_mga3_el_thy
## 151/190: Comparing analyses for: wt_ll_cf_minus_mga3_el_thy
## 152/190: Comparing analyses for: wt_ll_cg_minus_mga3_el_thy
## 153/190: Comparing analyses for: wt_ll_thy_minus_mga3_el_thy
## 154/190: Comparing analyses for: wt_st_thy_minus_mga3_el_thy
## 155/190: Comparing analyses for: mga3_ll_thy_minus_mga3_ll_c
## 156/190: Comparing analyses for: mga3_st_thy_minus_mga3_ll_c
## 157/190: Comparing analyses for: wt_el_thy_minus_mga3_ll_c
## 158/190: Comparing analyses for: wt_ll_c_minus_mga3_ll_c
## 159/190: Comparing analyses for: wt_ll_cf_minus_mga3_ll_c
## 160/190: Comparing analyses for: wt_ll_cg_minus_mga3_ll_c
## 161/190: Comparing analyses for: wt_ll_thy_minus_mga3_ll_c
## 162/190: Comparing analyses for: wt_st_thy_minus_mga3_ll_c
## 163/190: Comparing analyses for: mga3_st_thy_minus_mga3_ll_thy
## 164/190: Comparing analyses for: wt_el_thy_minus_mga3_ll_thy
## 165/190: Comparing analyses for: wt_ll_c_minus_mga3_ll_thy
## 166/190: Comparing analyses for: wt_ll_cf_minus_mga3_ll_thy
## 167/190: Comparing analyses for: wt_ll_cg_minus_mga3_ll_thy
## 168/190: Comparing analyses for: wt_ll_thy_minus_mga3_ll_thy
## 169/190: Comparing analyses for: wt_st_thy_minus_mga3_ll_thy
## 170/190: Comparing analyses for: wt_el_thy_minus_mga3_st_thy
## 171/190: Comparing analyses for: wt_ll_c_minus_mga3_st_thy
## 172/190: Comparing analyses for: wt_ll_cf_minus_mga3_st_thy
## 173/190: Comparing analyses for: wt_ll_cg_minus_mga3_st_thy
## 174/190: Comparing analyses for: wt_ll_thy_minus_mga3_st_thy
## 175/190: Comparing analyses for: wt_st_thy_minus_mga3_st_thy
## 176/190: Comparing analyses for: wt_ll_c_minus_wt_el_thy
## 177/190: Comparing analyses for: wt_ll_cf_minus_wt_el_thy
## 178/190: Comparing analyses for: wt_ll_cg_minus_wt_el_thy
## 179/190: Comparing analyses for: wt_ll_thy_minus_wt_el_thy
## 180/190: Comparing analyses for: wt_st_thy_minus_wt_el_thy
## 181/190: Comparing analyses for: wt_ll_cf_minus_wt_ll_c
## 182/190: Comparing analyses for: wt_ll_cg_minus_wt_ll_c
## 183/190: Comparing analyses for: wt_ll_thy_minus_wt_ll_c
## 184/190: Comparing analyses for: wt_st_thy_minus_wt_ll_c
## 185/190: Comparing analyses for: wt_ll_cg_minus_wt_ll_cf
## 186/190: Comparing analyses for: wt_ll_thy_minus_wt_ll_cf
## 187/190: Comparing analyses for: wt_st_thy_minus_wt_ll_cf
## 188/190: Comparing analyses for: wt_ll_thy_minus_wt_ll_cg
## 189/190: Comparing analyses for: wt_st_thy_minus_wt_ll_cg
## 190/190: Comparing analyses for: wt_st_thy_minus_wt_ll_thy
tiff(file="figures/compare_methods_heatmap.tiff", res=90, width=8, height=8, units='in')
supercrazytown$comparison$heat
dev.off()## X11cairo
## 2An email from Kayla
I was wondering if you could give me a list of genes that are expressed at the same level as mac (spy_0668) in the WT 5448 in THY at LL. I can see from IGV that the number of reads aligned to this gene is lower than other genes, and therefore it is probably expressed at a lower level. I am interested in finding other genes that are expressed at comparable levels. The overall goal is to identify a gene that can be used as an alternative reference gene for qPCR
wt_ll_thy_table = limma_results$wt_ll_thy
target_expr = wt_ll_thy_table["M5005_Spy0668",]
target_expr## logFC AveExpr t P.Value
## M5005_Spy0668 2.777874 1.733432 12.78465 0.0000000000000001503
## adj.P.Val B qvalue
## M5005_Spy0668 0.0000000000000001824 27.39945 0.000000000000000004467## so lets pull everyone from 0.15 to 0.25?
targets = subset(wt_ll_thy_table, AveExpr <= 0.25 & AveExpr >= 0.15)
targets## logFC AveExpr t P.Value adj.P.Val
## M5005_Spy1035 1.3262458 0.1879516 4.686222 0.00002615 0.00002851
## M5005_Spy1717 -1.2805048 0.2094715 -4.321379 0.00008511 0.00009198
## M5005_Spy0523 -0.5825061 0.2287656 -2.320545 0.02492000 0.02590000
## M5005_Spy1202 0.3723053 0.1735476 1.464843 0.14990000 0.15380000
## B qvalue
## M5005_Spy1035 1.6694462 0.0000006982
## M5005_Spy1717 0.7154376 0.0000022530
## M5005_Spy0523 -4.6819451 0.0006343000
## M5005_Spy1202 -6.2783824 0.0037680000Perform some ontology analyses
summary(crazytown$all_pairwise$mga2_ll_thy_minus_wt_ll_thy)## Length Class Mode
## 0 NULL NULLlimma_results = crazytown$all_tables
available_comparisons = names(limma_results)
mga2_ll_thy_top = limma_subset(limma_results$wt_ll_thy_minus_mga2_ll_thy)$up
mga2_ll_thy_bottom = limma_subset(limma_results$wt_ll_thy_minus_mga2_ll_thy)$down
gene_widths = get_genelengths("reference/genome/gas.gff", key='locus_tag')
gene_widths$ID = gsub('Spy_', 'Spy', gene_widths$ID)
goids = microbes_go
goids$name = gsub("Spy_", "Spy", goids$name)
colnames(goids) = c("ID","GO")
up_goseq = simple_goseq(mga2_ll_thy_top, lengths=gene_widths, goids=goids)## simple_goseq() makes some pretty hard assumptions about the data it is fed:
## It requires 2 tables, one of GOids which must have columns (gene)ID and GO(category)
## The other table is of gene lengths with columns (gene)ID and (gene)width.
## Other columns are fine, but ignored.
## Using the length data to fill in the de vector.
## Using manually entered categories.
## Calculating the p-values...
## Calculating q-values
## Filling godata table with term information, this takes a while.## [1] "Testing that go categories are defined."
## [1] "Removing undefined categories."
## [1] "Gathering synonyms."
## [1] "Gathering secondary ids."
## [1] "Gathering category definitions."## Making pvalue plots for the ontologies.
up_goseq$bpp_plot
down_goseq = simple_goseq(mga2_ll_thy_bottom, lengths=gene_widths, goids=goids)## simple_goseq() makes some pretty hard assumptions about the data it is fed:
## It requires 2 tables, one of GOids which must have columns (gene)ID and GO(category)
## The other table is of gene lengths with columns (gene)ID and (gene)width.
## Other columns are fine, but ignored.
## Using the length data to fill in the de vector.
## Using manually entered categories.
## Calculating the p-values...
## Calculating q-values
## Filling godata table with term information, this takes a while.## [1] "Testing that go categories are defined."
## [1] "Removing undefined categories."
## [1] "Gathering synonyms."
## [1] "Gathering secondary ids."
## [1] "Gathering category definitions."## Making pvalue plots for the ontologies.
down_goseq$bpp_plot
up_cluster = simple_clusterprofiler(mga2_ll_thy_top, goids=goids, gff="reference/genome/gas.gff")## Using GO mapping data located in GO2EG.rda
## Starting MF(molecular function) analysis## The minimum observed adjusted pvalue is: 0.027788## Warning in if (class(all_mf_phist) != "try-error") {: the condition has
## length > 1 and only the first element will be used## The minimum observed adjusted pvalue is: 1.000000## Starting BP(biological process) analysis## The minimum observed adjusted pvalue is: 0.000533## Warning in if (class(all_bp_phist) != "try-error") {: the condition has
## length > 1 and only the first element will be used## The minimum observed adjusted pvalue is: 0.016158## Starting CC(cellular component) analysis## The minimum observed adjusted pvalue is: 0.016763
## The minimum observed adjusted pvalue is: 0.402306## Warning in if (class(all_cc_phist) != "try-error") {: the condition has
## length > 1 and only the first element will be used## Attempting to include the cnetplots from clusterProfiler.
## They fail often, if this is causing errors, set:
## include_cnetplots to FALSE
## cnetplot just failed for the MF ontology. Do not be concerned with the previous error.
## cnetplot just failed for the CC ontology. Do not be concerned with the previous error.
up_cluster$bp_all_barplot
KEGG Mapping
thy_el_comp1_kegg = thy_el_comp1$table$logFC
names(thy_el_comp1_kegg) = rownames(thy_el_comp1$table)
thy_el_comp2_kegg = thy_el_comp2$table$logFC
names(thy_el_comp2_kegg) = rownames(thy_el_comp2$table)
thy_el_comp3_kegg = thy_el_comp3$table$logFC
names(thy_el_comp3_kegg) = rownames(thy_el_comp3$table)
thy_el_comp3_path = hpgl_pathview(thy_el_comp3_kegg, species="spz", indir="pathview_in", outdir="kegg_thy_el_comp3", string_from="_Spy", string_to="_Spy_", filenames="pathname")
thy_ll_comp1_kegg = thy_ll_comp1$table$logFC
names(thy_ll_comp1_kegg) = rownames(thy_ll_comp1$table)
thy_ll_comp2_kegg = thy_ll_comp2$table$logFC
names(thy_ll_comp2_kegg) = rownames(thy_ll_comp2$table)
thy_ll_comp2_path = hpgl_pathview(thy_ll_comp2_kegg, species="spz", indir="pathview_in", outdir="kegg_thy_ll_comp2", string_from="_Spy", string_to="_Spy_", filenames="pathname")
thy_ll_comp3_kegg = thy_ll_comp3$table$logFC
names(thy_ll_comp3_kegg) = rownames(thy_ll_comp3$table)
thy_ll_comp3_path = hpgl_pathview(thy_ll_comp3_kegg, species="spz", indir="pathview_in", outdir="kegg_thy_ll_comp3", string_from="_Spy", string_to="_Spy_", filenames="pathname")
thy_st_comp1_kegg = thy_st_comp1$table$logFC
names(thy_st_comp1_kegg) = rownames(thy_st_comp1$table)
thy_st_comp2_kegg = thy_st_comp2$table$logFC
names(thy_st_comp2_kegg) = rownames(thy_st_comp2$table)
thy_st_comp2_path = hpgl_pathview(thy_st_comp2_kegg, species="spz", indir="pathview_in", outdir="kegg_thy_st_comp2", string_from="_Spy", string_to="_Spy_", filenames="pathname")
thy_st_comp3_kegg = thy_st_comp3$table$logFC
names(thy_st_comp3_kegg) = rownames(thy_st_comp3$table)
thy_st_comp3_path = hpgl_pathview(thy_st_comp3_kegg, species="spz", indir="pathview_in", outdir="kegg_thy_st_comp3", string_from="_Spy", string_to="_Spy_", filenames="pathname")
c_ll_comp1_kegg = c_ll_comp1$table$logFC
names(c_ll_comp1_kegg) = rownames(c_ll_comp1$table)
c_ll_comp2_kegg = c_ll_comp2$table$logFC
names(c_ll_comp2_kegg) = rownames(c_ll_comp2$table)
c_ll_comp2_path = hpgl_pathview(c_ll_comp2_kegg, species="spz", indir="pathview_in", outdir="kegg_c_ll_comp2", string_from="_Spy", string_to="_Spy_", filenames="pathname")
c_ll_comp3_kegg = c_ll_comp3$table$logFC
names(c_ll_comp3_kegg) = rownames(c_ll_comp3$table)
c_ll_comp3_path = hpgl_pathview(c_ll_comp3_kegg, species="spz", indir="pathview_in", outdir="kegg_c_ll_comp3", string_from="_Spy", string_to="_Spy_", filenames="pathname")
thyc_ll_comp_kegg = thyc_ll_comp$table$logFC
names(thyc_ll_comp_kegg) = rownames(thyc_ll_comp$table)
thyc_ll_comp_path = hpgl_pathview(thyc_ll_comp_kegg, species="spz", indir="pathview_in", outdir="kegg_thyc_ll_comp", string_from="_Spy", string_to="_Spy_", filenames="pathname")
save(list = ls(all=TRUE), file="RData")Quick comparison of two mutants
mga1mga3_merged = merge(thy_el_comp1$table, thy_el_comp3$table, by="row.names")
write_xls(mga1mga3_merged, sheet="mga1mga3", file="merged.xls")
mga1_mga3_comp = mga1mga3_merged[,c("logFC.x","logFC.y")]
hpgl_scatter(mga1_mga3_comp)
hpgl_cor(mga1_mga3_comp, method="robust")## logFC.x logFC.y
## logFC.x 1.0000000 0.1505812
## logFC.y 0.1505812 1.0000000cor.test(mga1_mga3_comp[,1], mga1_mga3_comp[,2], method="spearman")## Warning in cor.test.default(mga1_mga3_comp[, 1], mga1_mga3_comp[, 2],
## method = "spearman"): Cannot compute exact p-value with ties##
## Spearman's rank correlation rho
##
## data: mga1_mga3_comp[, 1] and mga1_mga3_comp[, 2]
## S = 898360000, p-value = 0.0000000000004918
## alternative hypothesis: true rho is not equal to 0
## sample estimates:
## rho
## 0.1663927mga1mga2_merged = merge(thy_el_comp1$table, thy_el_comp2$table, by="row.names")
write_xls(mga1mga2_merged, sheet="mga1mga2", file="merged.xls")
mga1_mga2_comp = mga1mga2_merged[,c("logFC.x","logFC.y")]
hpgl_scatter(mga1_mga2_comp)
hpgl_cor(mga1_mga2_comp, method="robust")## logFC.x logFC.y
## logFC.x 1.0000000 0.1248792
## logFC.y 0.1248792 1.0000000cor.test(mga1_mga2_comp[,1], mga1_mga2_comp[,2], method="spearman")## Warning in cor.test.default(mga1_mga2_comp[, 1], mga1_mga2_comp[, 2],
## method = "spearman"): Cannot compute exact p-value with ties##
## Spearman's rank correlation rho
##
## data: mga1_mga2_comp[, 1] and mga1_mga2_comp[, 2]
## S = 949670000, p-value = 0.0000002724
## alternative hypothesis: true rho is not equal to 0
## sample estimates:
## rho
## 0.1187793mga2mga3_merged = merge(thy_el_comp2$table, thy_el_comp3$table, by="row.names")
write_xls(mga2mga3_merged, sheet="mga2mga3", file="merged.xls")
mga2_mga3_comp = mga2mga3_merged[,c("logFC.x","logFC.y")]
hpgl_scatter(mga2_mga3_comp)
hpgl_cor(mga2_mga3_comp, method="robust")## logFC.x logFC.y
## logFC.x 1.0000000 0.4712134
## logFC.y 0.4712134 1.0000000cor.test(mga2_mga3_comp[,1], mga2_mga3_comp[,2], method="spearman")## Warning in cor.test.default(mga2_mga3_comp[, 1], mga2_mga3_comp[, 2],
## method = "spearman"): Cannot compute exact p-value with ties##
## Spearman's rank correlation rho
##
## data: mga2_mga3_comp[, 1] and mga2_mga3_comp[, 2]
## S = 610970000, p-value < 0.00000000000000022
## alternative hypothesis: true rho is not equal to 0
## sample estimates:
## rho
## 0.4330635mga2_el_up = subset(thy_el_comp2$table, logFC >= 1.0)
mga3_el_up = subset(thy_el_comp3$table, logFC >= 1.0)
mga2mga3_el_up_inter = merge(mga2_el_up, mga3_el_up, by="row.names")
mga2_el_down = subset(thy_el_comp2$table, logFC <= -1.0)
mga3_el_down = subset(thy_el_comp3$table, logFC <= -1.0)
mga2mga3_el_down_inter = merge(mga2_el_down, mga3_el_down, by="row.names")
write.csv(mga2mga3_el_up_inter, file="excel/mga2mga3_el_up.csv")
write.csv(mga2mga3_el_down_inter, file="excel/mga2mga3_el_down.csv")
mga2_ll_up = subset(thy_ll_comp2$table, logFC >= 1.0)
mga3_ll_up = subset(thy_ll_comp3$table, logFC >= 1.0)
mga2mga3_ll_up_inter = merge(mga2_ll_up, mga3_ll_up, by="row.names")
mga2_ll_down = subset(thy_ll_comp2$table, logFC <= -1.0)
mga3_ll_down = subset(thy_ll_comp3$table, logFC <= -1.0)
mga2mga3_ll_down_inter = merge(mga2_ll_down, mga3_ll_down, by="row.names")
write.csv(mga2mga3_ll_up_inter, file="excel/mga2mga3_ll_up.csv")
write.csv(mga2mga3_ll_down_inter, file="excel/mga2mga3_ll_down.csv")
mga2_st_up = subset(thy_st_comp2$table, logFC >= 1.0)
mga3_st_up = subset(thy_st_comp3$table, logFC >= 1.0)
mga2mga3_st_up_inter = merge(mga2_st_up, mga3_st_up, by="row.names")
mga2_st_down = subset(thy_st_comp2$table, logFC <= -1.0)
mga3_st_down = subset(thy_st_comp3$table, logFC <= -1.0)
mga2mga3_st_down_inter = merge(mga2_st_down, mga3_st_down, by="row.names")
write.csv(mga2mga3_st_up_inter, file="excel/mga2mga3_st_up.csv")
write.csv(mga2mga3_st_down_inter, file="excel/mga2mga3_st_down.csv")
mga2_cll_up = subset(c_ll_comp2$table, logFC >= 1.0)
mga3_cll_up = subset(c_ll_comp3$table, logFC >= 1.0)
mga2mga3_cll_up_inter = merge(mga2_cll_up, mga3_cll_up, by="row.names")
mga2_cll_down = subset(c_ll_comp2$table, logFC <= -1.0)
mga3_cll_down = subset(c_ll_comp3$table, logFC <= -1.0)
mga2mga3_cll_down_inter = merge(mga2_cll_down, mga3_cll_down, by="row.names")
write.csv(mga2mga3_cll_up_inter, file="excel/mga2mga3_cll_up.csv")
write.csv(mga2mga3_cll_down_inter, file="excel/mga2mga3_cll_down.csv")## Use circos to visualize changes from wt to mga deletion at:
## 1. Early log
## 2. Late log
## 3. Stationary
head(thy_el_comp2$table)## logFC AveExpr t P.Value
## M5005_Spy1715 -6.920108 7.297489 -33.544858 0.000000000014650662
## M5005_Spy1719 -6.867694 11.493174 -35.742558 0.000000000007833118
## M5005_Spy1718 -6.556882 6.246703 -38.013097 0.000000000004263734
## M5005_Spy1714 -6.302030 5.784534 -20.421110 0.000000001903435824
## M5005_Spy1629 -5.889767 1.706075 -9.985522 0.000001686552313031
## M5005_Spy1631 -5.575451 1.299794 -8.511380 0.000007082625520590
## adj.P.Val B
## M5005_Spy1715 0.000000005458837 17.026666
## M5005_Spy1719 0.000000003648275 17.730139
## M5005_Spy1718 0.000000003648275 17.810542
## M5005_Spy1714 0.000000186636892 12.405441
## M5005_Spy1629 0.000016624587086 5.688056
## M5005_Spy1631 0.000047124754803 4.306565el_thy_information_table = merge(thy_el_comp2$table, genes, by.x="row.names", by.y="row.names")
el_thy_circos = el_thy_information_table[,c("ID","start","end","logFC")]
el_thy_circos$chr1 = "chr1"
el_thy_circos = el_thy_circos[,c("chr1","start","end","logFC")]
write.table(el_thy_circos, file="circos/data/el_thy_mut2.txt", quote=FALSE, row.names=FALSE, col.names=FALSE)
ll_thy_information_table = merge(thy_ll_comp2$table, genes, by.x="row.names", by.y="row.names")
ll_thy_circos = ll_thy_information_table[,c("ID","start","end","logFC")]
ll_thy_circos$chr1 = "chr1"
ll_thy_circos = ll_thy_circos[,c("chr1","start","end","logFC")]
write.table(ll_thy_circos, file="circos/data/ll_thy_mut2.txt", quote=FALSE, row.names=FALSE, col.names=FALSE)
st_thy_information_table = merge(thy_st_comp2$table, genes, by.x="row.names", by.y="row.names")
st_thy_circos = st_thy_information_table[,c("ID","start","end","logFC")]
st_thy_circos$chr1 = "chr1"
st_thy_circos = st_thy_circos[,c("chr1","start","end","logFC")]
write.table(st_thy_circos, file="circos/data/st_thy_mut2.txt", quote=FALSE, row.names=FALSE, col.names=FALSE)
head(thy_el_comp3$table)## logFC AveExpr t P.Value
## M5005_Spy1719 -10.481307 9.687092 -37.976270 0.000000000008036267
## M5005_Spy1718 -4.598989 7.221753 -34.541410 0.000000000019915687
## M5005_Spy1720 -4.508313 7.023127 -30.368908 0.000000000068160131
## M5005_Spy1715 -3.713541 8.905666 -24.661642 0.000000000495021315
## M5005_Spy1714 -3.529493 7.179075 -17.565657 0.000000012189593944
## M5005_Spy1631 -3.164139 2.466895 -5.790644 0.000202008290996425
## adj.P.Val B
## M5005_Spy1719 0.00000001497156 15.6757986
## M5005_Spy1718 0.00000001855146 16.3176983
## M5005_Spy1720 0.00000004232744 15.3233775
## M5005_Spy1715 0.00000023055618 13.7123195
## M5005_Spy1714 0.00000454184270 10.6132114
## M5005_Spy1631 0.00263175836452 0.9525042el_thy_information_table = merge(thy_el_comp3$table, genes, by.x="row.names", by.y="row.names")
el_thy_circos = el_thy_information_table[,c("ID","start","end","logFC")]
el_thy_circos$chr1 = "chr1"
el_thy_circos = el_thy_circos[,c("chr1","start","end","logFC")]
write.table(el_thy_circos, file="circos/data/el_thy_mut3.txt", quote=FALSE, row.names=FALSE, col.names=FALSE)
ll_thy_information_table = merge(thy_ll_comp3$table, genes, by.x="row.names", by.y="row.names")
ll_thy_circos = ll_thy_information_table[,c("ID","start","end","logFC")]
ll_thy_circos$chr1 = "chr1"
ll_thy_circos = ll_thy_circos[,c("chr1","start","end","logFC")]
write.table(ll_thy_circos, file="circos/data/ll_thy_mut3.txt", quote=FALSE, row.names=FALSE, col.names=FALSE)
st_thy_information_table = merge(thy_st_comp3$table, genes, by.x="row.names", by.y="row.names")
st_thy_circos = st_thy_information_table[,c("ID","start","end","logFC")]
st_thy_circos$chr1 = "chr1"
st_thy_circos = st_thy_circos[,c("chr1","start","end","logFC")]
write.table(st_thy_circos, file="circos/data/st_thy_mut3.txt", quote=FALSE, row.names=FALSE, col.names=FALSE)(Hopefully) quick request from Kayla.
Can I get a venn diagram of the following:
Comparison of the list of genes generated in the DE analysis that are significant (ie: Log 2 greater than or equal to 1 or -1) between mutant 2 (transposon) and mutant 3 (insertional) that are in:
THY at EL THY at LL THY at ST C Media at LL Comparison using the list of genes that are significant and present in both mutants from THY LL and C Media LL
Is there a way to generate a list of these genes that are present in each circle of the venn diagram? yes, see below.
You wanted me to remind you to double check the significance of the data using your new scripts done
## Restate goal: mutant 2 vs mutant 3, thy media, early log
## Restate goal: mutant 2 vs mutant 3, thy media, late log
## Restate goal: mutant 2 vs mutant 3, thy media, stationary
## Restate goal: mutant 2 vs mutant 3, C media, late log
tables = crazytown$all_tables
first = tables$mga3_el_thy_minus_mga2_el_thy
second = tables$mga3_ll_thy_minus_mga2_ll_thy
third = tables$mga3_st_thy_minus_mga2_st_thy
fourth = tables$mga3_ll_c_minus_mga2_ll_c
## universe[GroupA.l & GroupB.l & !GroupD.l]
first_up = as.vector(rownames(subset(first, logFC >= 1.0)))
second_up = as.vector(rownames(subset(second, logFC >= 1.0)))
third_up = as.vector(rownames(subset(third, logFC >= 1.0)))
fourth_up = as.vector(rownames(subset(fourth, logFC >= 1.0)))
first_down = as.vector(rownames(subset(first, logFC <= -1.0)))
second_down = as.vector(rownames(subset(second, logFC <= -1.0)))
third_down = as.vector(rownames(subset(third, logFC <= -1.0)))
fourth_down = as.vector(rownames(subset(fourth, logFC <= -1.0)))
uni = unique(c(rownames(first), rownames(second), rownames(third), rownames(fourth)))
fup = uni %in% first_up
sup = uni %in% second_up
tup = uni %in% third_up
foup = uni %in% fourth_up
fdown = uni %in% first_down
sdown = uni %in% second_down
tdown = uni %in% third_down
fodown = uni %in% fourth_down
## Pairwise venns
venn(list(mga32_el_thy=first_up, mga32_ll_thy=second_up))
first_second = uni[fup & sup]
first_second## [1] "M5005_Spy0158" "M5005_Spy0034" "M5005_SpyT0065" "M5005_SpyT0067"
## [5] "M5005_Spy1139" "M5005_Spy1761" "M5005_Spy0986" "M5005_Spy1759"
## [9] "M5005_Spy1786" "M5005_Spy0142" "M5005_Spy1138" "M5005_Spy1137"
## [13] "M5005_Spy0890" "M5005_Spy0157" "M5005_Spy0884" "M5005_Spy1760"
## [17] "M5005_Spy1497" "M5005_Spy1715" "M5005_Spy1498" "M5005_Spy0024"
## [21] "M5005_Spy0027" "M5005_Spy0694" "M5005_Spy0140" "M5005_Spy0913"
## [25] "M5005_Spy0139" "M5005_SpyT0064" "M5005_Spy1214" "M5005_Spy0028"
## [29] "M5005_Spy0889" "M5005_Spy1819" "M5005_Spy0177" "M5005_Spy1539"
## [33] "M5005_Spy1667" "M5005_Spy0025" "M5005_Spy0668" "M5005_Spy1762"
## [37] "M5005_Spy0029" "M5005_Spy0141" "M5005_Spy0914" "M5005_Spy1714"
## [41] "M5005_Spy0023" "M5005_Spy0026" "M5005_Spy0031" "M5005_Spy1510"
## [45] "M5005_Spy0460" "M5005_Spy1500" "M5005_Spy1821" "M5005_Spy0355"
## [49] "M5005_Spy1749" "M5005_Spy0798" "M5005_Spy0030" "M5005_Spy1718"
## [53] "M5005_Spy0351" "M5005_Spy0022" "M5005_Spy1739" "M5005_Spy1643"
## [57] "M5005_Spy0803" "M5005_Spy0459" "M5005_Spy1665" "M5005_Spy0800"
## [61] "M5005_Spy0797" "M5005_Spy0802" "M5005_Spy1721" "M5005_Spy0799"
## [65] "M5005_Spy0113" "M5005_Spy1644"venn(list(mga32_el_thy=first_up, mga32_st_thy=third_up))
first_third = uni[fup & tup]
first_third## [1] "M5005_Spy0158" "M5005_Spy0034" "M5005_Spy1793" "M5005_Spy1791"
## [5] "M5005_SpyT0067" "M5005_Spy1139" "M5005_Spy1761" "M5005_Spy1759"
## [9] "M5005_Spy1786" "M5005_Spy0142" "M5005_Spy1138" "M5005_Spy1137"
## [13] "M5005_Spy0890" "M5005_Spy0157" "M5005_Spy0884" "M5005_Spy1760"
## [17] "M5005_Spy1629" "M5005_Spy1497" "M5005_Spy1715" "M5005_Spy1498"
## [21] "M5005_Spy0024" "M5005_Spy0027" "M5005_Spy0694" "M5005_Spy1789"
## [25] "M5005_Spy0140" "M5005_Spy0913" "M5005_Spy0139" "M5005_Spy1214"
## [29] "M5005_Spy0889" "M5005_Spy0176" "M5005_Spy0041" "M5005_Spy0177"
## [33] "M5005_Spy1820" "M5005_Spy1531" "M5005_Spy1539" "M5005_Spy1667"
## [37] "M5005_Spy0025" "M5005_Spy1747" "M5005_Spy1762" "M5005_Spy0029"
## [41] "M5005_Spy0141" "M5005_Spy0914" "M5005_Spy1714" "M5005_Spy0023"
## [45] "M5005_Spy0026" "M5005_Spy0031" "M5005_Spy1510" "M5005_Spy1668"
## [49] "M5005_Spy0170" "M5005_Spy1556" "M5005_Spy1500" "M5005_Spy1630"
## [53] "M5005_Spy0355" "M5005_Spy1749" "M5005_Spy0798" "M5005_Spy1687"
## [57] "M5005_Spy0030" "M5005_Spy1718" "M5005_Spy1744" "M5005_Spy0351"
## [61] "M5005_Spy0022" "M5005_Spy0143" "M5005_Spy0459" "M5005_Spy1631"
## [65] "M5005_Spy1665" "M5005_Spy1633" "M5005_Spy1403" "M5005_Spy0797"
## [69] "M5005_Spy1634" "M5005_Spy1509" "M5005_Spy1632" "M5005_Spy1721"
## [73] "M5005_Spy1644" "M5005_Spy1635"venn(list(mga32_el_thy=first_up, mga32_c_ll=fourth_up))
first_fourth = uni[fup & foup]
first_fourth## [1] "M5005_SpyT0067" "M5005_Spy1139" "M5005_Spy0142" "M5005_Spy1629"
## [5] "M5005_Spy1715" "M5005_Spy0140" "M5005_Spy0139" "M5005_Spy0141"
## [9] "M5005_Spy1630" "M5005_Spy0355" "M5005_Spy1053" "M5005_Spy1739"
## [13] "M5005_Spy1631" "M5005_Spy1633" "M5005_Spy1634" "M5005_Spy1731"
## [17] "M5005_Spy1632" "M5005_Spy1721" "M5005_Spy1635"venn(list(mga32_ll_thy=second_up, mga32_st_thy=third_up))
second_third = uni[sup & tup]
second_third## [1] "M5005_Spy0158" "M5005_Spy0034" "M5005_SpyT0067" "M5005_Spy1139"
## [5] "M5005_Spy1761" "M5005_Spy1759" "M5005_Spy1786" "M5005_Spy0142"
## [9] "M5005_Spy1138" "M5005_Spy1137" "M5005_Spy0890" "M5005_Spy0157"
## [13] "M5005_Spy0884" "M5005_Spy1760" "M5005_Spy1497" "M5005_Spy1715"
## [17] "M5005_Spy1498" "M5005_Spy0024" "M5005_Spy0027" "M5005_Spy0694"
## [21] "M5005_Spy0140" "M5005_Spy0913" "M5005_Spy0139" "M5005_Spy1214"
## [25] "M5005_Spy0889" "M5005_Spy0177" "M5005_Spy1539" "M5005_Spy1667"
## [29] "M5005_Spy0025" "M5005_Spy1762" "M5005_Spy0029" "M5005_Spy0141"
## [33] "M5005_Spy0914" "M5005_Spy1714" "M5005_Spy0023" "M5005_Spy0026"
## [37] "M5005_Spy0031" "M5005_Spy1510" "M5005_Spy1500" "M5005_Spy1828"
## [41] "M5005_Spy0355" "M5005_Spy1749" "M5005_Spy0798" "M5005_Spy0030"
## [45] "M5005_Spy1718" "M5005_Spy0351" "M5005_Spy0022" "M5005_Spy1052"
## [49] "M5005_Spy0459" "M5005_Spy1665" "M5005_Spy0797" "M5005_Spy1499"
## [53] "M5005_Spy1863" "M5005_Spy1721" "M5005_Spy1578" "M5005_Spy1649"
## [57] "M5005_Spy1644" "M5005_Spy0144" "M5005_Spy0858"venn(list(mga32_ll_thy=second_up, mga32_c_ll=fourth_up))
second_fourth = uni[sup & foup]
second_fourth## [1] "M5005_SpyT0067" "M5005_Spy1139" "M5005_Spy0142" "M5005_Spy1715"
## [5] "M5005_Spy0140" "M5005_Spy0139" "M5005_Spy0141" "M5005_Spy0355"
## [9] "M5005_Spy1739" "M5005_Spy1721" "M5005_Spy0144"venn(list(mga32_st_thy=third_up, mga32_c_ll=fourth_up))
third_fourth = uni[tup & foup]
third_fourth## [1] "M5005_SpyT0067" "M5005_Spy1139" "M5005_Spy0142" "M5005_Spy1629"
## [5] "M5005_Spy1715" "M5005_Spy0140" "M5005_Spy0139" "M5005_Spy0141"
## [9] "M5005_Spy1630" "M5005_Spy0355" "M5005_Spy1631" "M5005_Spy1633"
## [13] "M5005_Spy1634" "M5005_Spy1632" "M5005_Spy1721" "M5005_Spy0492"
## [17] "M5005_Spy1628" "M5005_Spy1638" "M5005_Spy1635" "M5005_Spy0144"
## [21] "M5005_Spy0274" "M5005_Spy1637" "M5005_Spy1636"geneNames = rownames(first)
GroupA = first_up
GroupA.i <- which(geneNames %in% GroupA)
GroupB = second_up
GroupB.i <- which(geneNames %in% GroupB)
GroupC = third_up
GroupC.i <- which(geneNames %in% GroupC)
GroupD = fourth_up
GroupD.i <- which(geneNames %in% GroupD)
input <-list(GroupA,GroupB,GroupC,GroupD)
input.i <-list(A=GroupA.i,B=GroupB.i,C=GroupC.i,D=GroupD.i)
venn(input)
GroupA.f <- geneNames %in% GroupA
GroupB.f <- geneNames %in% GroupB
GroupC.f <- geneNames %in% GroupC
GroupD.f <- geneNames %in% GroupD
input.df <- data.frame(A=GroupA.f,B=GroupB.f,C=GroupC.f,D=GroupD.f)
head(input.df)## A B C D
## 1 FALSE FALSE FALSE FALSE
## 2 TRUE TRUE TRUE FALSE
## 3 TRUE TRUE TRUE FALSE
## 4 TRUE TRUE FALSE FALSE
## 5 TRUE FALSE TRUE FALSE
## 6 TRUE FALSE TRUE FALSEvenn(input.df)
venn(input, showSetLogicLabel=TRUE)
universe <- unique(c(GroupA,GroupB,GroupC,GroupD))
GroupA.l <-universe %in% GroupA
GroupB.l <-universe %in% GroupB
GroupC.l <-universe %in% GroupC
GroupD.l <-universe %in% GroupD
## Genes that are in GroupA and in GroupB but not in GroupD (unification
## of sets III0 and II00 in the venn diagram:
universe[GroupA.l & GroupB.l & !GroupD.l]## [1] "M5005_Spy0158" "M5005_Spy0034" "M5005_SpyT0065" "M5005_Spy1761"
## [5] "M5005_Spy0986" "M5005_Spy1759" "M5005_Spy1786" "M5005_Spy1138"
## [9] "M5005_Spy1137" "M5005_Spy0890" "M5005_Spy0157" "M5005_Spy0884"
## [13] "M5005_Spy1760" "M5005_Spy1497" "M5005_Spy1498" "M5005_Spy0024"
## [17] "M5005_Spy0027" "M5005_Spy0694" "M5005_Spy0913" "M5005_SpyT0064"
## [21] "M5005_Spy1214" "M5005_Spy0028" "M5005_Spy0889" "M5005_Spy1819"
## [25] "M5005_Spy0177" "M5005_Spy1539" "M5005_Spy1667" "M5005_Spy0025"
## [29] "M5005_Spy0668" "M5005_Spy1762" "M5005_Spy0029" "M5005_Spy0914"
## [33] "M5005_Spy1714" "M5005_Spy0023" "M5005_Spy0026" "M5005_Spy0031"
## [37] "M5005_Spy1510" "M5005_Spy0460" "M5005_Spy1500" "M5005_Spy1821"
## [41] "M5005_Spy1749" "M5005_Spy0798" "M5005_Spy0030" "M5005_Spy1718"
## [45] "M5005_Spy0351" "M5005_Spy0022" "M5005_Spy1643" "M5005_Spy0803"
## [49] "M5005_Spy0459" "M5005_Spy1665" "M5005_Spy0800" "M5005_Spy0797"
## [53] "M5005_Spy0802" "M5005_Spy0799" "M5005_Spy0113" "M5005_Spy1644"require.auto("VennDiagram")
up_plot = venn.diagram(
list(el_thy=first_up,
ll_thy=second_up,
st_thy=third_up,
ll_c=fourth_up),
"four_up.tiff")
up_plot2 = venn(
list(el_thy=first_up,
ll_thy=second_up,
st_thy=third_up,
ll_c=fourth_up),
)
down_plot = venn.diagram(
list(el_thy=first_down,
ll_thy=second_down,
st_thy=third_down,
ll_c=fourth_down),
"four_down.tiff")