pmapFromTranscriptF: Faster pmapFromTranscript
In ORFik: Open Reading Frames in Genomics

Description Usage Arguments Details Value Examples

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.

1	pmapFromTranscriptF(x, transcripts, removeEmpty = FALSE)

`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.

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.

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

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)