annotateLoops {diffloop} | R Documentation |
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).
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)
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 |
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.
A loops object with an additional row 'loop.type' in the rowData slot
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)