setup_GSEA: prepare files for GSEA analysis

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

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 = getInPASOutputDirectory(),
  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 InPAS analysis results. 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

library(limma)
path <- system.file("extdata", package = "InPAS")
load(file.path(path, "eset.MAQC.rda"))
tags <- colnames(eset@PDUI)
g <- factor(gsub("\\..*$", "", tags))
design <- model.matrix(~ -1 + g)
colnames(design) <- c("Brain", "UHR")
contrast.matrix <- makeContrasts(
  contrasts = "Brain-UHR",
  levels = design
)
res <- test_dPDUI(
  eset = eset,
  method = "limma",
  normalize = "none",
  design = design,
  contrast.matrix = contrast.matrix
)
gp1 <- c("Brain.auto", "Brain.phiX")
gp2 <- c("UHR.auto", "UHR.phiX")
groupList <- list(Brain = gp1, UHR = gp2)
setup_GSEA(res,
  groupList = groupList,
  outdir = tempdir(),
  preranked = TRUE,
  rankBy = "P.value"
)

jianhong/InPAS documentation built on Nov. 5, 2024, 7:45 a.m.