FeatureEnrichment: Calculate empirical p-value for genomic feature enrichment

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

Calculate empirical p-value for genomic feature enrichment

Description

Calculate empirical p-value for genomic feature enrichment

Usage

FeatureEnrichment(
  bedFile,
  species = "hsapiens",
  N = 1000,
  tss = c(-3000, 3000),
  sys = c("win", "")
)

Arguments

bedFile	String with path to bedfile to analyze. Must be a bed file
species	string indicating genus/species of genome. One of "hsapiens" or "mmusculus"
N	numeric indicating number of iterations
tss	numeric vector of length 2 indicating the promoter region around the tss site (default= c(-3000,3000))
sys	string indicating opertating system. - Not working at the moment, currently only works for windows running windows subsystem for linux with bedtools installed

Value

Data frame with p-values and adjusted p-values (BH corrected) for each genomic feature

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