loopGenes: Determine genes contained within loops

Description Usage Arguments Details Value Examples

Description

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

Usage

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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

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# 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)

Bioconductor-mirror/diffloop documentation built on June 1, 2017, 7:35 a.m.