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]