loadExonCountData {SeqGSEA} | R Documentation |
This function is used to load (sub-)exon count data. Exon count data can
be got by the Python script count_in_exons.py
.
loadExonCountData(case.files, control.files)
case.files |
a character vector containing the exon count file names for case samples |
control.files |
a character vector containing the exon count file names for control samples |
You may need the Python script count_in_exons.py (released with this package)
to generate your exon count files from read mapping results (say BAM files).
The detailed usage can be obtained by simply typing
python \path\to\count_in_exons.py
. Users can also use other scripts or
software for exon read counting.
The format of the exon count file is:
GeneName1:001[tab]Count11 GeneName1:002[tab]Count12 ... GeneName1:00N[tab]Count1N GeneName2:001[tab]Count21 ...
This function returns a ReadCountSet object.
Xi Wang, xi.wang@newcastle.edu.au
newReadCountSet
,
ReadCountSet-class
library(SeqGSEA) dat.dir = system.file("extdata", package="SeqGSEA", mustWork=TRUE) case.pattern <- "^SC" ctrl.pattern <- "^SN" case.files <- dir(dat.dir, pattern=case.pattern, full.names = TRUE) control.files <- dir(dat.dir, pattern=ctrl.pattern, full.names = TRUE) ## Not run: RCS <- loadExonCountData(case.files, control.files) RCS ## End(Not run)