rownames(hs_annot) <- make.names(paste0(hs_annot[["ensembl_transcript_id"]], ".", hs_annot[["transcript_version"]]), unique=TRUE)
salmon_expt <- create_expt(metadata="sample_sheets/rnaseq_samples.xlsx",
gene_info=hs_annot, file_column="salmonfile")## Reading the sample metadata.## The sample definitions comprises: 9, 12 rows, columns.## Reading count tables.## Reading salmon data with tximport.## Finished reading count tables.## Matched 81155 annotations and counts.## Bringing together the count matrix and gene information.## Some annotations were lost in merging, setting them to 'undefined'.kallisto_expt <- create_expt(metadata="sample_sheets/rnaseq_samples.xlsx",
gene_info=hs_annot, file_column="kallistofile")## Reading the sample metadata.## The sample definitions comprises: 9, 12 rows, columns.## Reading count tables.## Reading kallisto inputs with tximport.## Finished reading count tables.## Matched 93422 annotations and counts.## Bringing together the count matrix and gene information.## Some annotations were lost in merging, setting them to 'undefined'.## Using limma's removeBatchEffect to visualize before/after batch inclusion.## Finished running DE analyses, collecting outputs.## Comparing analyses 1/1: Rv_vs_Control## Using limma's removeBatchEffect to visualize before/after batch inclusion.## Finished running DE analyses, collecting outputs.## Comparing analyses 1/1: Rv_vs_Control## Writing a legend of columns.## Working on table 1/1: Rv_vs_Control## Writing a legend of columns.
## Working on table 1/1: Rv_vs_Control## If you wish to reproduce this exact build of hpgltools, invoke the following:## > git clone http://github.com/abelew/hpgltools.git## > git reset 1b009834267dea125ee94934203413fbd606e783## R> packrat::restore()## This is hpgltools commit: Mon Apr 23 14:59:56 2018 -0400: 1b009834267dea125ee94934203413fbd606e783this_save <- paste0(gsub(pattern="\\.Rmd", replace="", x=rmd_file), "-v", ver, ".rda.xz")
message(paste0("Saving to ", this_save))## Saving to 02_kallisto_vs_salmon-v20180306.rda.xzR version 3.4.4 (2018-03-15)
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: stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: ruv(v.0.9.7) and hpgltools(v.2018.03)
loaded via a namespace (and not attached): nlme(v.3.1-137), bitops(v.1.0-6), matrixStats(v.0.53.1), devtools(v.1.13.5), bit64(v.0.9-7), doParallel(v.1.0.11), RColorBrewer(v.1.1-2), rprojroot(v.1.3-2), GenomeInfoDb(v.1.14.0), tools(v.3.4.4), backports(v.1.1.2), R6(v.2.2.2), rpart(v.4.1-13), Hmisc(v.4.1-1), DBI(v.0.8), lazyeval(v.0.2.1), BiocGenerics(v.0.24.0), mgcv(v.1.8-23), colorspace(v.1.3-2), nnet(v.7.3-12), withr(v.2.1.2), gridExtra(v.2.3), DESeq2(v.1.18.1), bit(v.1.1-12), compiler(v.3.4.4), preprocessCore(v.1.40.0), Biobase(v.2.38.0), htmlTable(v.1.11.2), xml2(v.1.2.0), DelayedArray(v.0.4.1), checkmate(v.1.8.5), scales(v.0.5.0.9000), DEoptimR(v.1.0-8), robustbase(v.0.92-8), readr(v.1.1.1), genefilter(v.1.60.0), commonmark(v.1.4), stringr(v.1.3.0), digest(v.0.6.15), foreign(v.0.8-70), rmarkdown(v.1.9), XVector(v.0.18.0), base64enc(v.0.1-3), pkgconfig(v.2.0.1), htmltools(v.0.3.6), limma(v.3.34.9), htmlwidgets(v.1.2), rlang(v.0.2.0.9001), rstudioapi(v.0.7), RSQLite(v.2.1.0), BiocParallel(v.1.12.0), acepack(v.1.4.1), RCurl(v.1.95-4.10), magrittr(v.1.5), GenomeInfoDbData(v.1.0.0), Formula(v.1.2-2), Matrix(v.1.2-14), Rcpp(v.0.12.16), munsell(v.0.4.3), S4Vectors(v.0.16.0), stringi(v.1.1.7), yaml(v.2.1.18), edgeR(v.3.20.9), SummarizedExperiment(v.1.8.1), zlibbioc(v.1.24.0), rhdf5(v.2.22.0), plyr(v.1.8.4), grid(v.3.4.4), blob(v.1.1.1), parallel(v.3.4.4), ggrepel(v.0.7.0), lattice(v.0.20-35), splines(v.3.4.4), pander(v.0.6.1), annotate(v.1.56.2), hms(v.0.4.2), locfit(v.1.5-9.1), knitr(v.1.20), pillar(v.1.2.1), GenomicRanges(v.1.30.3), rjson(v.0.2.15), corpcor(v.1.6.9), geneplotter(v.1.56.0), codetools(v.0.2-15), stats4(v.3.4.4), XML(v.3.98-1.11), evaluate(v.0.10.1), latticeExtra(v.0.6-28), data.table(v.1.10.4-3), foreach(v.1.4.4), gtable(v.0.2.0), ggplot2(v.2.2.1), openxlsx(v.4.0.17), xtable(v.1.8-2), roxygen2(v.6.0.1), survival(v.2.42-3), tibble(v.1.4.2), iterators(v.1.0.9), AnnotationDbi(v.1.40.0), memoise(v.1.1.0), IRanges(v.2.12.0), tximport(v.1.6.0), cluster(v.2.0.7-1) and sva(v.3.26.0)