countOverlapsW {ORFik} | R Documentation

## CountOverlaps with weights

### Description

Similar to countOverlaps, but takes an optional weight column. This is usually the score column

### Usage

    countOverlapsW(query, subject, weight = NULL, ...)

### Arguments

`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

### Value

a named vector of number of overlaps to subject weigthed by 'weight' column.

### See Also

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()`

### Examples

    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")

[Package ORFik version 1.10.13 Index]