overlapsToCoverage {ORFik} | R Documentation

## Get overlaps and convert to coverage list

### Description

Get overlaps and convert to coverage list

### Usage

    overlapsToCoverage(gr, reads, keep.names = TRUE, type = "any")

### Arguments

`gr` | a `GRanges` of 5' utrs or transcripts.
`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.

### Value

a Rle, one list per group with # of hits per position.

### See Also

Other ExtendGenomicRanges: `asTX`, `coveragePerTiling`, `pmapFromTranscriptF`, `reduceKeepAttr`, `tile1`, `txSeqsFromFa`, `windowPerGroup`

### Examples

    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)

[Package ORFik version 1.2.1 Index]