startRegion: Start region as GRangesList

Description Usage Arguments Details Value See Also Examples

View source: R/ORFs_helpers.R

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

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

Examples

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## 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)

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