RNAseq of L.panamensis: Parasite Gene Ontology.

index.html annotation.html macrophage_estimation_parasite.html macrophage_expression_parasite.html

In this document, we will perform a series of differential expression analyses using the data which survived sample estimation.

1 Gene Ontology searches

Lets set up some simple data sets for goseq/clusterProfiler/topGO

I think a bunch of the material in this sheet is actually now obsolete.

1.1 Extracting ontology annotations from the TriTrypDB

## goseq uses the gene lengths, clusterprofiler and topgo don't
## gene_lengths <- all_genes[,c("geneid","genesize")]
## colnames(gene_lengths) <- c("ID", "width")
colnames(lp_lengths) <- c("ID", "width")
## go_ids needs to be a 2 column data frame with names 'ID', 'GO' which are
## gene names and GO names respectively.  I actually think I made my goseq() function
## smart enough that this is no longer needed, but nonetheless.

## go_ids <- read.table("reference/go/tcruzi_all_go.tab.gz", header=0, sep="\t")
## colnames(go_ids) <- c("ID","GO","ontology","term","source")
## Since there are multiple sources, I am doing a unique of the table...
## go_ids <- unique(go_ids[,c("ID","GO")])
## goid_file <- "reference/go/topgo_goids.tab.gz"

## colnames(lp_goids) <- c("ID", "GO")
lp_go <- lp_goids[, c("ID","GO")]
lp_go$ID <- paste0("exon_", lp_go$ID)
lp_go$ID <- paste0(lp_go$ID, ".1")

test_sig <- macro_batch_sig[["limma"]][["ups"]][["macro_chr-sh"]]

## Error in eval(expr, envir, enclos): object 'macro_batch_sig' not found

dim(test_sig)

## Error in eval(expr, envir, enclos): object 'test_sig' not found

## hmm maybe there are insufficient genes for gene ontology...
##macrobatch_shch_up_goseq <- simple_goseq(sig_genes=test_sig,
##                                         go_db=lp_go,
##                                         length_db=lp_lengths)
##macrobatch_shch_up_goseq <- sm(simple_goseq(sig_genes=macrobatch$limma$ups$macro_sh_vs_macro_ch,
##                                            go_db=lp_goids, length_db=lp_lengths))
##macrobatch_shch_up_excel <- sm(write_goseq_data(macrobatch_shch_up_goseq,
##                                                excel=paste0("excel/macrobatch_shch_up_goseq-v", ver, ".xlsx")))