coverageByWindow {ORFik} | R Documentation

## Compute coverage for every GRangesList subset.

### Description

This is similar to [GenomicFeatures::coverageByTranscript()], but it adds: automatic sorting of the windows, fix for some rare cases when subsetting fails on minus/plus strands and security that subseting of windows will always return values (zeros) istead of out of bounds error.

### Usage

    coverageByWindow(x, windows, ignore.strand = FALSE, is.sorted = FALSE,
      keep.names = TRUE)

### Arguments

`x` | the cigar of the reads
`windows` | (GRangesList) of transcripts or CDS or other ranges that will be subseting coverage of 'x'
`ignore.strand` | (logical) Whether to consider all reads to be "*".
`is.sorted` | (logical), is windows already sorted.
`keep.names` | logical (T), keep names and meta cols

### Details

Minus strand is already flipped so that the most 5' position on the window is the first position in the returned Rle.

### Value

(RleList) of positional counts of 'x' ranges overlapping each consecutive position of the elements of 'windows'

### Examples

    cds <- GenomicRanges::GRangesList(
      GenomicRanges::GRanges(seqnames = "chr1",
                             ranges = IRanges::IRanges(100, 200),
                             strand = "+"))
    reads <- GenomicRanges::GRanges(
      seqnames = "chr1",
      ranges =  IRanges::IRanges(c(100, 150), c(110, 160)),
      strand = "+")
    ORFik:::coverageByWindow(reads, cds)

[Package ORFik version 1.2.1 Index]