pmapFromTranscriptF: Faster pmapFromTranscript

In JokingHero/ORFik: Open Reading Frames in Genomics

Faster pmapFromTranscript

Description

Map range coordinates between features in the transcriptome and genome (reference) space. 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.

Usage

pmapFromTranscriptF(x, transcripts, removeEmpty = FALSE)

Arguments

x	IRangesList/IRanges/GRanges to map to genomic coordinates
transcripts	a GRangesList to map against (the genomic coordinates)
removeEmpty	a logical, remove non hit exons, else they are set to 0. That is all exons in the reference that the transcript coordinates do not span.

Details

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

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)

JokingHero/ORFik documentation built on April 7, 2024, 2:59 a.m.