diffloop (version 1.0.2)

loopGenes: Determine genes contained within loops

Description

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

Usage

loopGenes(dlo, genesGR)
## S3 method for class 'loops,GRanges':
loopGenes(dlo, genesGR)

Arguments

dlo

A loops object

genesGR

A GRanges object of genes with mcol 'id'

Value

• A matrix of comma separated gene names

Details

Function that annotates all loops. 'NA' if looping between chromosomes. Otherwise, all gene names that are contained within a loop. 'None' if no genes are in the loop body. If there are multiple, the function returns a comma separated list. The length of the object returned by this function should be the same length as the number of rows in the loops slot.

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)