customGO: Custom GO Function

In kevincjnixon/BinfTools: Useful functions for standard analyses

Custom GO Function

Description

Perform a hypergeometric enrichment test for a custom gene set

Usage

customGO(
  genes,
  gmt,
  gsName = "custom GeneSet",
  bg = NULL,
  sp = "human",
  FDR = TRUE,
  byRegion = FALSE,
  enr = "pos",
  significant = TRUE,
  minp = 1e-300
)

Arguments

genes	character vector of genes to be queried
gmt	Named list of gene set(s) to be analyzed for enrichment
gsName	Character specifying geneSet source - to be incorportated into output and help indicate source of gene sets
bg	character vector of genes indicating the background of genes. If left NULL, argument 'sp' will indicate species and assume all genes are in background.
sp	character of either "human" or "mouse" indicating the species. This will provide the number of background genes if bg=NULL.
FDR	Boolean indicating if p-values should be FDR corrected (Benjamini-Hochberg). Default is TRUE.
byRegion	Boolean. If query genes has duplicate gene symbols, set to TRUE to remove duplicates (relevant only if query genes are from annotated peaks from genomic data). Default=FALSE.
enr	character of either "pos" or "neg" indicating if significance should be calculated for positive or negative hypergeometric enrichment, respectively. default="pos".
significant	Boolean indicating if only significant (p<0.05) results should be returned. defaulte=TRUE.
minp	numeric indicating the minimum p-value possible reported (to avoid zeros)

Value

Data.frame of same structure of results table from GO_GEM() when returnRes=TRUE.

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