buildBroadGSEAcomm: Build the command-line command to run BROAD GSEA

In bedapub/ribiosGSEA: Gene-Set Enrichment Analysis Tools in Ribios

Build the command-line command to run BROAD GSEA

Description

Build the command-line command to run BROAD GSEA

Usage

buildBroadGSEAcomm(
  gseaJar,
  javaBin,
  rnkFiles,
  gmtFile,
  chipFile,
  nperm = 1000L,
  collapse = FALSE,
  plotTopX = 25,
  outdir = "./",
  addShebang = TRUE
)

Arguments

gseaJar	Character string, full file name of BROAD GSEA (gene permutation) jar file
javaBin	Character string, java binary file
rnkFiles	Character string, rank files
gmtFile	A GMT file encoding GMT files to be used
chipFile	A CHIP file encoding feature annotation
nperm	Integer, number of permutations
collapse	Logical, whether to collapse duplicated features
plotTopX	Integer, top gene-sets to be visualized
outdir	Character string, the path of output
addShebang	Logical, whether to add Shebang to the script The command builds command-line command to run gene-permutation GSEA over many rank files.

bedapub/ribiosGSEA documentation built on March 30, 2023, 3:26 p.m.