prepare4GSEA: prepare the files for GSEA analysis

In InPAS: InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

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)

InPAS documentation built on Nov. 8, 2020, 5:03 p.m.