coveragePerTiling {ORFik}R Documentation

Get coverage per group

Description

It tiles each GRangesList group, and finds hits per position

Usage

coveragePerTiling(grl, reads, is.sorted = FALSE, keep.names = TRUE)

Arguments

grl

a GRangesList of 5' utrs or transcripts.

reads

a GAlignment or GRanges object of RiboSeq, RnaSeq etc

is.sorted

logical (F), is grl sorted.

keep.names

logical (T), keep names or not.

Value

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

See Also

Other ExtendGenomicRanges: asTX, overlapsToCoverage, pmapFromTranscriptF, reduceKeepAttr, tile1, txSeqsFromFa, windowPerGroup

Examples

ORF <- GRanges(seqnames = "1",
               ranges = IRanges(start = c(1, 10, 20),
                                end = c(5, 15, 25)),
               strand = "+")
grl <- GRangesList(tx1_1 = ORF)
RFP <- GRanges("1", IRanges(25, 25), "+")
coveragePerTiling(grl, RFP)


[Package ORFik version 1.2.1 Index]