prepare4GSEA: prepare the files for GSEA analysis

Description Usage Arguments Value Author(s) Examples

View source: R/prepare4GSEA.R

Description

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

Usage

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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

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    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 April 29, 2020, 5:19 a.m.