slurmEdgeRcommand: Return the SLURM command to run the edgeR script

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

Return the SLURM command to run the edgeR script

Description

Return the SLURM command to run the edgeR script

Usage

slurmEdgeRcommand(
  dgeList,
  designMatrix,
  contrastMatrix,
  outdir = "edgeR_output",
  outfilePrefix = "an-unnamed-project-",
  mps = FALSE,
  limmaVoom = FALSE,
  appendGmt = NULL,
  qos = c("short", "interactive", "normal"),
  params = "",
  debug = FALSE
)

Arguments

dgeList	An DGEList object with counts, genes, and samples
designMatrix	The design matrix to model the data
contrastMatrix	The contrast matrix matching the design matrix
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 Slurm. Available values include short (recommended default, running time cannot exceed 3 hours), interactive (useful if you wish to get the results from an interactive session), and normal (useful if the job is expected to run more than three hours.) using srun and the 'interaction' queue of jobs instead of using sbatch.
params	Character, further parameters to pass to sbatch, for instance "–partition ANOTHER_PARITION"
debug	Logical, if TRUE, the source code of Rscript is used instead of the installed version. The option is passed to edgeRcommand. This function wraps the function edgeRcommand to return the command needed to start a SLURM 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)
 slurmEdgeRcommand(y, designMatrix=myDesign, contrastMatrix=myContrast,
     outfilePrefix="test", outdir=tempdir())

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