distToCds: Get distances between ORF ends and starts of their...

In JokingHero/ORFik: Open Reading Frames in Genomics

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: computeFeatures(), computeFeaturesCage(), countOverlapsW(), disengagementScore(), distToTSS(), entropy(), floss(), fpkm(), fpkm_calc(), fractionLength(), initiationScore(), insideOutsideORF(), isInFrame(), isOverlapping(), kozakSequenceScore(), orfScore(), rankOrder(), ribosomeReleaseScore(), ribosomeStallingScore(), startRegion(), startRegionCoverage(), stopRegion(), subsetCoverage(), translationalEff()

Examples

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

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.