R/8b_runChipEnrich.R

In Mathelab/ALTRE: Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data

#' Enrichment analysis using chip-Enrich package
#' to identify putative pathways of interest for further
#' investigation
#'

#library(chipenrich)

#mypeaks=as.data.frame(consPeaksAnnotated$consPeaksAnnotated[2:20,])[,1:3]
#colnames(mypeaks)[1]="chrom"
#myenrich=chipenrich(peaks=mypeaks, out_name="chipenrich", genome="hg19",
#	genesets=c('GOBP','GOCC','GOMF'), locusdef = "nearest_tss",
#	method='chipenrich', read_length=50)