loopGenes: Determine genes contained within loops

In aryeelab/diffloop: Identifying differential DNA loops from chromatin topology data

Description

loopGenes determines all gene bodies partially or fully contained in a loop.

Usage

loopGenes(dlo, genesGR)

## S4 method for signature 'loops,GRanges'
loopGenes(dlo, genesGR)

## S4 method for signature 'loops,missing'
loopGenes(dlo, genesGR)

Arguments

dlo	A loops object
genesGR	A GRanges object of genes in first mcol.

Details

Function that annotates all loops. If there are multiple, the function returns a comma separated list. Adds a "loopGenes" column to the rowData slot. If the genesGR is left blank, diffloop will use protein coding genes for human from hg19.

Value

A matrix of comma separated gene names

Examples

# Determine the genes housed in the loops from our example
genes <- getHumanGenes()
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
loops.small <- loopGenes(loops.small,genes)

aryeelab/diffloop documentation built on May 12, 2019, 3:42 a.m.