distToCds {ORFik} | R Documentation

## Get distances between ORF ends and starts of their transcripts cds.

### Description

Will calculate distance between each ORF end and begining of the corresponding cds (main ORF). Matching is done by transcript names. This is applicable practically to the upstream (fiveUTRs) ORFs only. The cds start site, will be presumed to be on + 1 of end of fiveUTRs.

### Usage

    distToCds(ORFs, fiveUTRs, cds = NULL)

### Arguments

`ORFs` | orfs as `GRangesList`, names of orfs must be transcript names
`fiveUTRs` | fiveUTRs as `GRangesList`, remember to use CAGE version of 5' if you did CAGE reassignment!
`cds` | cds' as `GRangesList`, only add if you have ORFs going into CDS.

### Value

an integer vector, +1 means one base upstream of cds, -1 means 2nd base in cds, 0 means orf stops at cds start.

### References

doi: 10.1074/jbc.R116.733899

### See Also

Other features: `computeFeaturesCage`, `computeFeatures`, `disengagementScore`, `distToTSS`, `entropy`, `floss`, `fpkm_calc`, `fpkm`, `fractionLength`, `initiationScore`, `insideOutsideORF`, `isInFrame`, `isOverlapping`, `kozakSequenceScore`, `orfScore`, `rankOrder`, `ribosomeReleaseScore`, `ribosomeStallingScore`, `startRegionCoverage`, `startRegion`, `subsetCoverage`, `translationalEff`

### Examples

    grl <- GRangesList(tx1_1 = GRanges("1", IRanges(1, 10), "+"))
    fiveUTRs <- GRangesList(tx1 = GRanges("1", IRanges(1, 20), "+"))
    distToCds(grl, fiveUTRs)

[Package ORFik version 1.4.1 Index]