pmapFromTranscriptF {ORFik}R Documentation

Faster pmapFromTranscript

Description

This version tries to fix the shortcommings of GenomicFeature's version. Much faster and uses less memory. Implemented as dynamic program optimized c++ code.

Usage

pmapFromTranscriptF(x, transcripts, removeEmpty = FALSE)

Arguments

x

IRangesList/IRanges/GRanges to map to genomic coordinates

transcripts

a GRangesList to map agains

removeEmpty

a logical, remove non hit exons, else they are set to 0.

Details

The length of x must be the same as length of transcripts. Only exception is if x have integer names like (1, 3, 3, 5), so that x[1] maps to 1, x[2] maps to transcript 3 etc.

Value

a GRangesList of mapped reads, names from ranges are kept.

Examples

ranges <- IRanges(start = c( 5, 6), end = c(10, 10))
seqnames = rep("chr1", 2)
strands = rep("-", 2)
grl <- split(GRanges(seqnames, IRanges(c(85, 70), c(89, 82)), strands),
             c(1, 1))
ranges <- split(ranges, c(1,1)) # both should be mapped to transcript 1
pmapFromTranscriptF(ranges, grl, TRUE)


[Package ORFik version 1.4.0 Index]