countOverlapsW {ORFik} | R Documentation |
Similar to countOverlaps, but takes an optional weight column. This is usually the score column
countOverlapsW(query, subject, weight = NULL, ...)
query |
IRanges, IRangesList, GRanges, GRangesList object. Usually transcript a transcript region. |
subject |
GRanges, GRangesList, GAlignment, usually reads. |
weight |
(default: NULL), if defined either numeric or character name of valid meta column in subject. If weight is single numeric, it is used for all. A normall weight is the score column given as weight = "score". GRanges("chr1", 1, "+", score = 5), would mean score column tells that this alignment region was found 5 times. |
... |
additional arguments passed to countOverlaps/findOverlaps |
a named vector of number of overlaps to subject weigthed by 'weight' column.
Other features:
computeFeaturesCage()
,
computeFeatures()
,
disengagementScore()
,
distToCds()
,
distToTSS()
,
entropy()
,
floss()
,
fpkm_calc()
,
fpkm()
,
fractionLength()
,
initiationScore()
,
insideOutsideORF()
,
isInFrame()
,
isOverlapping()
,
kozakSequenceScore()
,
orfScore()
,
rankOrder()
,
ribosomeReleaseScore()
,
ribosomeStallingScore()
,
startRegionCoverage()
,
startRegion()
,
stopRegion()
,
subsetCoverage()
,
translationalEff()
gr1 <- GRanges(seqnames="chr1", ranges=IRanges(start = c(4, 9, 10, 30), end = c(4, 15, 20, 31)), strand="+") gr2 <- GRanges(seqnames="chr1", ranges=IRanges(start = c(1, 4, 15, 25), end = c(2, 4, 20, 26)), strand=c("+"), score=c(10, 20, 15, 5)) countOverlaps(gr1, gr2) countOverlapsW(gr1, gr2, weight = "score")