metaboGSE: Gene set enrichment analysis

In metaboGSE: Gene Set Enrichment Analysis via Integration of Metabolic Networks and RNA-Seq Data

Description

This function performs the gene set enrichment analysis.

Usage

metaboGSE(
  scores,
  gene.sets = NULL,
  method = "perm",
  test = NA,
  nperm = 1000,
  nrand = 1000,
  mc.cores = 1,
  posthoc = TRUE,
  contrast = FALSE,
  prefix = NA,
  desc.data = NULL,
  cols = NULL,
  ltys = NULL
)

Arguments

scores	A list of scoreGeneDel objects.
gene.sets	A named list of gene sets for gene set enrichment analysis, or a vector of gene set IDs computed in scores. Default: NULL, all gene sets from scores.
method	Statistical testing method c("perm", "survival"). Default: "perm". "survial" may be used for exploration.
test	Type of test c("likelihood", "logrank", "wald"), when method = "survival". Default: "likelihood".
nperm	Number of permutations for testing, when method = "perm". Default: 10000.
nrand	Number of draws for random gene set generation, when method = "perm". Default: 1000.
mc.cores	The number of cores to use (at least 1), i.e. at most how many child processes will be run simultaneously. Default: 1.
posthoc	A logical value indicating if pairwise tests are performed. Default: TRUE.
contrast	A logical value indicating if the Newick-based contrast will be computed. Default: FALSE.
prefix	A string indicating prefix of output plots. Default: NA, no plot.
desc.data	A vector of descriptions of a priori KEGG pathway IDs. Default: NULL, KEGGREST will be called with internet connection required if gene.sets is KEGG pathway.
cols	Colors for conditions. Default: rainbow colors.
ltys	Line types for conditions. Default: incrementing line types in R.

Value

Gene set enrichment information

Examples

data(yarliSubmnets)

metaboGSE(yarliSubmnets[c('SH','SN')], gene.sets = "GO:0006696",
         method="perm", nperm=10, nrand=10)

metaboGSE documentation built on Oct. 23, 2020, 8:14 p.m.