prepare4GSEA {InPAS} | R Documentation

## prepare the files for GSEA analysis

### Description

output the log2 transformed delta PDUI txt file and chip file for GSEA analysis

### Usage

    prepare4GSEA(eset, groupList, Preranked=TRUE,
                 folder=".",
                 rnkFilename="InPAS.rnk",
                 chipFilename="InPAS.chip",
                 dataFilename="dPDUI.txt",
                 PhenFilename="group.cls")

### Arguments

`eset` | a UTR3eSet object
`groupList` | group list of tag names
`Preranked` | logical value, out preranked or not
`folder` | output folder
`rnkFilename` | filename of preranked file
`chipFilename` | filename of chip
`dataFilename` | filename of dataset
`PhenFilename` | filename of Phenotype labels

### Value

None

### Author(s)

Jianhong Ou

### Examples

        file <- system.file("extdata", "eset.MAQC.rda", package="InPAS")
        load(file)
        gp1=c("Brain.auto", "Brain.phiX")
        gp2=c("UHR.auto", "UHR.phiX")
        groupList <- list(Brain=gp1, UHR=gp2)
        prepare4GSEA(eset, groupList=groupList, Preranked=FALSE)

[Package InPAS version 1.18.0 Index]