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]