setup_GSEA {InPAS}

R Documentation

prepare files for GSEA analysis

Description

output the log2 transformed delta PDUI txt file, chip file, rank file and phynotype label file for GSEA analysis

Usage

setup_GSEA(
  eset,
  groupList,
  outdir,
  preranked = TRUE,
  rankBy = c("logFC", "P.value"),
  rnkFilename = "InPAS.rnk",
  chipFilename = "InPAS.chip",
  dataFilename = "dPDUI.txt",
  PhenFilename = "group.cls"
)

Arguments

eset	A UTR3eSet object, output of test_dPDUI()
groupList	A list of grouped sample tag names, with the group names as the list's name, such as list(groupA = c("sample_1", "sample_2", "sample_3"), groupB = c("sample_4", "sample_5", "sample_6"))
outdir	A character(1) vector, a path with write permission for storing the files for GSEA analysis. If it doesn't exist, it will be created.
preranked	A logical(1) vector, out preranked or not
rankBy	A character(1) vector, indicating how the gene list is ranked. It can be "logFC" or "P.value".
rnkFilename	A character(1) vector, specifying a filename for the preranked file
chipFilename	A character(1) vector, specifying a filename for the chip file
dataFilename	A character(1) vector, specifying a filename for the dataset file
PhenFilename	A character(1) vector, specifying a filename for the file containing samples' phenotype labels

Author(s)

Jianhong Ou, Haibo Liu

See Also

data formats for GSEA. https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats

Examples

if (interactive()) {
  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, 
               outdir = tempdir(),
               preranked = TRUE,
               rankBy = "logFC")
}

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