startRegionCoverage {ORFik} | R Documentation

## Start region coverage

### Description

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

### Usage

    startRegionCoverage(
      grl,
      RFP,
      tx = NULL,
      is.sorted = TRUE,
      upstream = 2L,
      downstream = 2L,
      weight = 1L
    )

### Arguments

`grl` | a `GRangesList` object with usually either leaders, cds', 3' utrs or ORFs
`RFP` | ribo seq reads as GAlignments, GRanges or GRangesList object
`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
`weight` | a vector (default: 1L, if 1L it is identical to countOverlaps()), if single number (!= 1), it applies for all, if more than one must be equal size of 'reads'. else it must be the string name of a defined meta column in subject "reads", that gives number of times a read was found. GRanges("chr1", 1, "+", score = 5), would mean "score" column tells that this alignment region was found 5 times.

### Details

If tx is null, then upstream will be force to 0 and downstream to a maximum of grl width. Since there is no reference for splicing.

### Value

a numeric vector of counts

### 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()`, `startRegion()`, `stopRegion()`, `subsetCoverage()`, `translationalEff()`

[Package ORFik version 1.12.13 Index]