distToTSS: Get distances between ORF Start and TSS of its transcript

In JokingHero/ORFik: Open Reading Frames in Genomics

Get distances between ORF Start and TSS of its transcript

Description

Matching is done by transcript names. This is applicable practically to any region in Transcript If ORF is not within specified search space in tx, this function will crash.

Usage

distToTSS(ORFs, tx)

Arguments

ORFs	orfs as GRangesList, names of orfs must be txname_[rank]
tx	transcripts as GRangesList.

Value

an integer vector, 1 means on TSS, 2 means second base of Tx.

References

doi: 10.1074/jbc.R116.733899

See Also

Other features: computeFeatures(), computeFeaturesCage(), countOverlapsW(), disengagementScore(), distToCds(), 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(5, 10), "+"))
tx <- GRangesList(tx1 = GRanges("1", IRanges(2, 20), "+"))
distToTSS(grl, tx)

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