stopRegion: Stop region as GRangesList

In JokingHero/ORFik: Open Reading Frames in Genomics

Stop region as GRangesList

Description

Get the stop region of each ORF / region. If you want the stop codon only, set downstream = 0 or just use stopCodons. Standard is 2 upstream and 2 downstream, a width 5 window centered at stop site.

Usage

stopRegion(grl, tx = NULL, is.sorted = TRUE, upstream = 2L, downstream = 2L)

Arguments

grl	a GRangesList object with usually either leaders, cds', 3' utrs or ORFs
tx	default NULL, a GRangesList of transcripts or (container region), names of tx must contain all grl names. The names of grl can also be the ORFik orf names. that is "txName_id"
is.sorted	logical (TRUE), is grl sorted.
upstream	an integer (2), relative region to get upstream from.
downstream	an integer (2), relative region to get downstream from

Details

If tx is null, then downstream will be forced to 0 and upstream to a minimum of -grl width (to the TSS). . Since there is no reference for splicing.

Value

a GRanges, or GRangesList object if any group had > 1 exon.

See Also

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

Examples

## ORF stop region
orf <- GRangesList(tx1 = GRanges("1", 200:300, "+"))
tx <- GRangesList(tx1 = GRanges("1",
                   IRanges(c(100, 305), c(300, 400)), "+"))
stopRegion(orf, tx, upstream = 6, downstream = 6)
## 2nd last codon of ORF
stopRegion(orf, tx, upstream = 6, downstream = -3)

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