loopGenes {diffloop} | R Documentation |
loopGenes
determines all gene bodies partially or fully contained
in a loop.
loopGenes(dlo, genesGR) ## S4 method for signature 'loops,GRanges' loopGenes(dlo, genesGR) ## S4 method for signature 'loops,missing' loopGenes(dlo, genesGR)
dlo |
A loops object |
genesGR |
A GRanges object of genes in first mcol. |
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.
A matrix of comma separated gene names
# 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)