loadExonCountData {SeqGSEA} | R Documentation

## Load Exon Count Data

### 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, xi.wang@newcastle.edu.au

### 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)

[Package SeqGSEA version 1.30.0 Index]