1 Sample estimation: 20170703
This block makes some graphs, normalizes the data, and replots the same graphs.
initial_plots <- sm(graph_metrics(parasite_expt))parasite_norm <- sm(normalize_expt(parasite_expt, transform="log2", norm="quant", convert="cpm", filter=TRUE))
norm_plots <- sm(graph_metrics(parasite_norm))1.1 Look at metrics
Now let us view some of them.
initial_plots$libsize
initial_plots$boxplot
initial_plots$density
initial_plots$corheat
norm_plots$corheat
norm_plots$disheat
norm_plots$pcaplot
2 Write metrics
Create an excel workbook of the various metrics with the following.
written <- sm(write_expt(parasite_expt, transform="log2", norm="quant", convert="cpm", filter=TRUE,
batch="raw", excel=paste0("excel/written-v", ver, ".xlsx")))pander::pander(sessionInfo())R version 3.4.1 (2017-06-30)
**Platform:** x86_64-pc-linux-gnu (64-bit)
locale: LC_CTYPE=en_US.utf8, LC_NUMERIC=C, LC_TIME=en_US.utf8, LC_COLLATE=en_US.utf8, LC_MONETARY=en_US.utf8, LC_MESSAGES=en_US.utf8, LC_PAPER=en_US.utf8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.utf8 and LC_IDENTIFICATION=C
attached base packages: parallel, stats4, stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: hpgltools(v.2017.01), TxDb.Lmajor.friedlin.TriTrypDB28(v.28.0), org.Lmajor.friedlin.eg.db(v.28.0), Leishmania.major.Friedlin(v.28.0), GO.db(v.3.4.1), OrganismDbi(v.1.18.0), GenomicFeatures(v.1.28.4), GenomicRanges(v.1.28.4), GenomeInfoDb(v.1.12.2), AnnotationDbi(v.1.38.2), IRanges(v.2.10.3), S4Vectors(v.0.14.3), Biobase(v.2.36.2) and BiocGenerics(v.0.22.0)
loaded via a namespace (and not attached): bitops(v.1.0-6), matrixStats(v.0.52.2), devtools(v.1.13.3), bit64(v.0.9-7), RColorBrewer(v.1.1-2), rprojroot(v.1.2), tools(v.3.4.1), backports(v.1.1.0), R6(v.2.2.2), KernSmooth(v.2.23-15), DBI(v.0.7), lazyeval(v.0.2.0), colorspace(v.1.3-2), withr(v.2.0.0), preprocessCore(v.1.38.1), bit(v.1.1-12), compiler(v.3.4.1), graph(v.1.54.0), xml2(v.1.1.1), DelayedArray(v.0.2.7), labeling(v.0.3), rtracklayer(v.1.36.4), scales(v.0.5.0), quadprog(v.1.5-5), RBGL(v.1.52.0), commonmark(v.1.4), stringr(v.1.2.0), digest(v.0.6.12), Rsamtools(v.1.28.0), rmarkdown(v.1.6), XVector(v.0.16.0), base64enc(v.0.1-3), pkgconfig(v.2.0.1), htmltools(v.0.3.6), limma(v.3.32.5), highr(v.0.6), rlang(v.0.1.2), RSQLite(v.2.0), BiocInstaller(v.1.26.1), bindr(v.0.1), gtools(v.3.5.0), BiocParallel(v.1.10.1), dplyr(v.0.7.2), RCurl(v.1.95-4.8), magrittr(v.1.5), GenomeInfoDbData(v.0.99.0), Matrix(v.1.2-11), Rcpp(v.0.12.12), munsell(v.0.4.3), edgeR(v.3.18.1), stringi(v.1.1.5), yaml(v.2.1.14), SummarizedExperiment(v.1.6.3), zlibbioc(v.1.22.0), Rtsne(v.0.13), plyr(v.1.8.4), grid(v.3.4.1), blob(v.1.1.0), ggrepel(v.0.6.5), crayon(v.1.3.2), lattice(v.0.20-35), Biostrings(v.2.44.2), pander(v.0.6.1), locfit(v.1.5-9.1), knitr(v.1.17), corpcor(v.1.6.9), reshape2(v.1.4.2), codetools(v.0.2-15), biomaRt(v.2.32.1), XML(v.3.98-1.9), glue(v.1.1.1), evaluate(v.0.10.1), data.table(v.1.10.4), foreach(v.1.4.3), testthat(v.1.0.2), gtable(v.0.2.0), assertthat(v.0.2.0), ggplot2(v.2.2.1), openxlsx(v.4.0.17), roxygen2(v.6.0.1), tibble(v.1.3.4), iterators(v.1.0.8), GenomicAlignments(v.1.12.2), memoise(v.1.1.0), bindrcpp(v.0.2) and directlabels(v.2017.03.31)
message(paste0("This is hpgltools commit: ", get_git_commit()))## If you wish to reproduce this exact build of hpgltools, invoke the following:## > git clone http://github.com/abelew/hpgltools.git## > git reset 739e4a10345a89efb17b37e7de07c5811491ccea## R> packrat::restore()## This is hpgltools commit: Thu Aug 31 11:24:06 2017 -0400: 739e4a10345a89efb17b37e7de07c5811491cceathis_save <- paste0(gsub(pattern="\\.Rmd", replace="", x=rmd_file), "-v", ver, ".rda.xz")
message(paste0("Saving to: ", this_save))## Saving to: 02_sample_estimation-v20170703.rda.xztmp <- sm(saveme(filename=this_save))