pmapFromTranscriptF {ORFik} | R Documentation

## 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 shortcommings 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)

[Package ORFik version 1.6.9 Index]