annotateLoops: Annotate loops as Enhancer-Promoter or CTCF-CTCF

In aryeelab/diffloop: Identifying differential DNA loops from chromatin topology data

Description

annotateLoops adds a column to the rowData slot of a loops object categorizing loops as either e-p (enhancer-promoter), p-p (promoter-promoter), e-e (enhancer-enhancer), ctcf (CTCF-CTCF) or none (no biological annotation).

Usage

annotateLoops(lto, ctcf, enhancer, promoter)

## S4 method for signature 'loops,GRanges,GRanges,GRanges'
annotateLoops(lto, ctcf, enhancer,
  promoter)

## S4 method for signature 'loops,missing,GRanges,GRanges'
annotateLoops(lto, ctcf, enhancer,
  promoter)

Arguments

lto	A loops object whose loops will be annotated
ctcf	GRanges object corresponding to locations of CTCF peaks
enhancer	GRanges object corresponding to locations of enhancer peaks
promoter	GRanges object corresponding to locations of promoter regions

Details

Function annotates loops where both anchors are near CTCF peaks or where one anchor is near an enhancer and the other near a promoter. Consider using functions addchr, rmchr, bedToGRanges, and padGRanges when setting up the 3 GRanges inputs. Provide a blank GRanges objects to ignore classification for one set.

Value

A loops object with an additional row 'loop.type' in the rowData slot

Examples

rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
ctcf_j <- system.file('extdata','Jurkat_CTCF_chr1.narrowPeak',package='diffloop')
ctcf <- rmchr(padGRanges(bedToGRanges(ctcf_j), pad = 1000))
h3k27ac_j <- system.file('extdata','Jurkat_H3K27ac_chr1.narrowPeak',package='diffloop')
h3k27ac <- rmchr(padGRanges(bedToGRanges(h3k27ac_j), pad = 1000))
promoter <- padGRanges(getHumanTSS(c('1')), pad = 1000)
# annotated_small <- annotateLoops(loops.small, ctcf, h3k27ac, promoter)

aryeelab/diffloop documentation built on May 12, 2019, 3:42 a.m.