loadExonCountData: Load Exon Count Data

In SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Description

This function is used to load (sub-)exon count data. Exon count data can be got by the Python script count_in_exons.py.

Usage

loadExonCountData(case.files, control.files)

Arguments

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

Details

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
...

Value

This function returns a ReadCountSet object.

Author(s)

Xi Wang, [e-mail]

See Also

newReadCountSet, ReadCountSet-class

Examples

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)

SeqGSEA documentation built on Nov. 8, 2020, 5:46 p.m.