lsfEdgeRcommand: Return the LSF command to run the edgeR script

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

Return the LSF command to run the edgeR script

Description

Return the LSF command to run the edgeR script

Usage

lsfEdgeRcommand(
  dgeList,
  designContrast,
  outdir = "edgeR_output",
  outfilePrefix = "an-unnamed-project-",
  mps = FALSE,
  limmaVoom = FALSE,
  appendGmt = NULL,
  qos = c("long", "preempty", "short"),
  rootPath = "~/apps/geneexpression",
  debug = FALSE,
  bsubFile = NULL
)

Arguments

dgeList	An DGEList object with counts, genes, and samples
designContrast	The DesignContrast object to model the data
outdir	Output directory of the edgeR script. Default value "edgeR_output".
outfilePrefix	Prefix of the output files. It can include directories, e.g. "data/outfile-". In case of NULL, temporary files will be created.
mps	Logical, whether molecular-phenotyping analysis is run.
limmaVoom	Logical, whether the limma-voom model is run instead of the edgeR model
appendGmt	NULL or character string, path to an additional GMT file for gene-set analysis. The option is passed to edgeRcommand.
qos	Character, specifying Quality of Service of LSF Available values include long, short, and preempty.
rootPath	Character string, the directory of geneexpression scripts, under which bin/ngsDge_edgeR.Rscript is found.
debug	Logical, if TRUE, the source code of Rscript is used instead of the installed version. The option is passed to edgeRcommand.
bsubFile	NULL or character string, file name that contains LSF jobs. If NULL, a file will be generated within the current directory following the pattern of outfilePrefix.bsub. This function wraps the function edgeRcommand to return the command needed to start a LSF job. It uses outdir to specify slurm output and error files as in the same directory of outdir. And the job name is set as the name of the output directory.

See Also

edgeRcommand

Examples

 mat <- matrix(rnbinom(100, mu=5, size=2), ncol=10)
 rownames(mat) <- sprintf("gene%d", 1:nrow(mat))
 myFac <- gl(2,5, labels=c("Control", "Treatment"))
 y <- edgeR::DGEList(counts=mat, group=myFac)
 myDesign <- model.matrix(~myFac); colnames(myDesign) <- levels(myFac)
 myContrast <- limma::makeContrasts(Treatment, levels=myDesign)
 myDesCon <- DesignContrast(designMatrix=myDesign, contrastMatrix=myContrast)
 lsfEdgeRcommand(y, designContrast=myDesCon,
     outfilePrefix="test", outdir=tempdir())
 ## remove the bsub file
 file.remove("test.bsub")

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.