overlapsToCoverage {ORFik} | R Documentation |
Get overlaps and convert to coverage list
overlapsToCoverage(gr, reads, keep.names = TRUE, type = "any")
gr |
a |
reads |
a GAlignment or GRanges object of RiboSeq, RnaSeq etc. |
keep.names |
logical (T), keep names or not. |
type |
a string (any), argument for countOverlaps. |
a Rle, one list per group with # of hits per position.
Other ExtendGenomicRanges: asTX
,
coveragePerTiling
,
reduceKeepAttr
, tile1
,
txSeqsFromFa
, windowPerGroup
ORF <- GRanges(seqnames = "1", ranges = IRanges(start = c(1, 10, 20), end = c(5, 15, 25)), strand = "+") names(ORF) <- "tx1" reads <- GRanges("1", IRanges(25, 25), "+") overlapsToCoverage(ORF, reads)