geneAssociation: Gene Association

In alexjgriffith/mulcal: To facilitate the analysis of multiple ChIP-Seq data sets

Description

Assosiate each ChIP enrinchement region with the closest peak within a bound defined by the user

Usage

geneAssociation(bedData, geneList, bounds, n = FALSE)

Arguments

bedData	three column data.frame
geneList	a data.frame loaded without a header from the refseq gene data base
bounds	c(A,B,C,D) Region 1 = (tss-A,tss+B) Region 2 = (ess-C ess+D)
n	Number of nodes to use.

Author(s)

Alexander Griffith [e-mail]

Source

https://github.com/alexjgriffith/mulcal

Examples

fileLocation="~/Dropbox/UTX-Alex/jan/"
bedData<-read.delim(paste(fileLocation,"combined_sorted.bed",sep=""),header=0)
geneList<-read.delim(paste(fileLocation,"hg19.RefSeqGenes.csv",sep=""))
genes<-geneAssociation(bedData,geneList,  c(50000,0,0,0))
write.table(cbind(bedData,unlist(t(lapply(genes, function(x) {if(identical(x,character(0))){"None"} else{x}})))) ,"combined_tagged_genes.bed" ,col.names=FALSE,row.names=FALSE,quote=FALSE,sep="\t")

alexjgriffith/mulcal documentation built on May 10, 2019, 8:53 a.m.