pmapFromTranscriptF {ORFik} | R Documentation |
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.
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)