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

Description Usage Arguments Value References See Also Examples

View source: R/sequence_features.R

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

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

Examples

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grl <- GRangesList(tx1_1 = GRanges("1", IRanges(5, 10), "+"))
tx <- GRangesList(tx1 = GRanges("1", IRanges(2, 20), "+"))
distToTSS(grl, tx)

ORFik documentation built on March 27, 2021, 6 p.m.