clusGO: Pathway Enrichment Analysis on Clusters

In kevincjnixon/BinfTools: Useful functions for standard analyses

Pathway Enrichment Analysis on Clusters

Description

Run Pathway Enrichment Analysis (same as GO_GEM()) on output from clusFigs()

Usage

clusGO(
  clusRes,
  species = "hsapiens",
  bg = rownames(clusRes),
  source = NULL,
  corr = "fdr",
  iea = FALSE,
  prefix = "ClusGO",
  ts = c(10, 500),
  pdf = TRUE,
  fig = TRUE,
  returnGost = FALSE,
  writeRes = TRUE,
  writeGem = FALSE,
  returnRes = FALSE,
  writeGene = FALSE
)

Arguments

clusRes	data.frame object that is output from clusFigs()
writeGene	Boolean indicating if the genes in each cluster should be written out to 'prefix_clustern.genes.txt". Default is FALSE.
...	Arguments for GO_GEM() see ?GO_GEM for details. bg is automatically set as rownames(clusRes).

Value

For each cluster, output from GO_GEM() is generated and output to "prefixclustern"

kevincjnixon/BinfTools documentation built on July 10, 2024, 11:46 a.m.