customGREAT: Function to perform GREAT analysis using custom gene sets

In kevincjnixon/ChIPATAC: Wrapper functions for useful genomic analyses like ChIP-seq or ATAC-seq.

Function to perform GREAT analysis using custom gene sets

Description

This function performs the binomial test on a given set of genomic regions and a custom gene set file

Usage

customGREAT(
  hits,
  gmt,
  TxDb,
  annoDb,
  promoter = F,
  tssRegion = c(-1000, 1000),
  parallel = T,
  returnCov = F,
  genCov = NULL,
  gsName = "customGMT",
  FDR = T,
  enr = "pos",
  significant = T
)

Arguments

hits	GenomicRanges object of regions to query, or string indicating the path to a bed file
gmt	Named list of gene sets of string indicating path/address to custom gene set (in gmt format)
TxDb	TxDb object corresponding to the genome build specific to the hits
annoDb	String indiciating the annotation DB object, i.e. "org.hs.eg.db"
promoter	Boolean indicating if analysis should be limited to hits annotated to only promoter regions (TRUE) or not (FALSE). Default is FALSE.
tssRegion	Numeric vector of length 2 indicating the size of the promoter region around the transcription start site (default is c(-1000,1000))
parallel	Boolean indicating if genomic coverage process should be run in parallel (requires packages 'parallel' and 'doparallel'). Only works for Windows at the moment. Default is TRUE.
returnCov	Boolean indicating if background coverage of each term in gmt should be returned. Default is FALSE. If you plan on running the same gmt file for multiple sets of regions, it is recommended you set returnCov=T for the first iteration and use the returned object in the genCov argument to save time.
genCov	Genomic coverage for each term in gmt file. Object returned if 'returnCov=T'. Default=NULL. Recommended to use if using same gmt file for multiple sets of regions.
gsName	String providing identifier for gene set name in results. Default="customGMT"
FDR	Boolean indicating if reported p-values should be FDR (BH) corrected. Default is TRUE.
enr	String indicating type of enrichment. Default="pos" for positive enrichment. Other options: "neg" for negative enrichment or "ts" for two-sided.
significant	Boolean indicating if only significant (p<0.05) results should be returned. Default=TRUE. FALSE returns all results.

Value

Data frame of results in the same format as BinfTools::GOGEM() results for compatibility with BinfTools.

kevincjnixon/ChIPATAC documentation built on May 25, 2023, 9:33 p.m.