loopGenes {diffloop}R Documentation

Determine genes contained within loops

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)


[Package diffloop version 1.18.0 Index]