startRegion {ORFik} | R Documentation

## 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: `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

    ## 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)

[Package ORFik version 1.12.13 Index]