startRegion: Start region as GRangesList

In JokingHero/ORFik: Open Reading Frames in Genomics

Start region as GRangesList

Description

Get the start region of each ORF. If you want the start codon only, set upstream = 0 or just use startCodons. Standard is 2 upstream and 2 downstream, a width 5 window centered at start site. since p-shifting is not 100 usually the reads from the start site.

Usage

startRegion(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 upstream will be forced to 0 and downstream to a maximum of grl width (3' UTR end for mRNAs). 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(), startRegionCoverage(), stopRegion(), subsetCoverage(), translationalEff()

Examples

## ORF start region
orf <- GRangesList(tx1 = GRanges("1", 200:300, "+"))
tx <- GRangesList(tx1 = GRanges("1",
                   IRanges(c(100, 200), c(195, 400)), "+"))
startRegion(orf, tx, upstream = 6, downstream = 6)
## 2nd codon of ORF
startRegion(orf, tx, upstream = -3, downstream = 6)

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