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. 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`, `disengagementScore`, `distToCds`, `distToTSS`, `entropy`, `floss`, `fpkm_calc`, `fpkm`, `fractionLength`, `initiationScore`, `insideOutsideORF`, `isInFrame`, `isOverlapping`, `kozakSequenceScore`, `orfScore`, `rankOrder`, `ribosomeReleaseScore`, `ribosomeStallingScore`, `startRegionCoverage`, `subsetCoverage`, `translationalEff`

[Package ORFik version 1.4.1 Index]