Automagically analyzes RNA-seq data and exports counts and results in R environment. Similar to the Rscript version, but will by default produce a dds object instead of writing results externally. Can currently only handle a single condition, with sampleTable columns "sampleName", "fileName", "condition".

DESeqAnalysis(dir, sample.table, name = NULL, workbook = FALSE,
  rdata = FALSE, flat.file = FALSE, ret = TRUE)

Arguments

dir

directory to create package in. [default: current working directory]

sample.table

path to sampleTable (or just name if it is in --dir) [default: sampleTable.txt]

name

path to directory for output of count and results tables [default: results]

rdata

save RData file of DESeq object to name [default: FALSE]

flat.file

save a flat version for use with HOMER

ret

return dds object [default: TRUE]

Value

DESeq2 dds object if ret(urn) is set to true.

Examples

Rscript deseq2.R -d /home/Documents/ -s sampleTable2.txt -n results_RNASeq
Rscript --dir /home2/Docs/ example2Package
Running DESeq2
Export All Things to Workbooks (openxlsx)
Add count tables
Save workbook
Writing as flat files (for HOMER usage)
Writing Results Matrices
Writing RData file