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. Matching is done by transcript names. This is applicable practically to the upstream (fiveUTRs) ORFs. The cds start site, will be presumed to be on + 1 of end of fiveUTRs.

### Usage

    distToCds(ORFs, fiveUTRs, cds = NULL, extension = NULL)

### Arguments

`ORFs` | orfs as `GRangesList`, names of orfs must be transcript names
`fiveUTRs` | fiveUTRs as `GRangesList`, must be original unchanged fiveUTRs
`cds` | cds' as `GRangesList`, only add if you used CageSeq to extend leaders
`extension` | Numeric that needs set to 0 if you did not use CageSeq if you used CageSeq to change tss' when finding the orfs, standard cage extension is 1000.

### 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`, `entropy`, `floss`, `fpkm_calc`, `fpkm`, `fractionLength`, `insideOutsideORF`, `isInFrame`, `isOverlapping`, `kozakSequenceScore`, `orfScore`, `rankOrder`, `ribosomeReleaseScore`, `ribosomeStallingScore`, `subsetCoverage`, `translationalEff`

### Examples

    grl <- GRangesList(tx1_1 = GRanges("1", IRanges(1, 10), "+"))
    fiveUTRs <- GRangesList(tx1 = GRanges("1", IRanges(1, 20), "+"))
    distToCds(grl, fiveUTRs, extension = 0)

[Package ORFik version 1.0.0 Index]