riboTISCoverageProportion {ORFik} | R Documentation

## Find proportion of reads per position in ORF TIS window

### Description

Proportion defined as: average count per position in -20,20 normalized by counts per gene

### Usage

    riboTISCoverageProportion(grl, tx, footprints, onlyProportion = FALSE,
      average = FALSE, pShifted = TRUE, keep.names = FALSE,
      upStart = if (pShifted) 5 else 20, downStop = if (pShifted) 20 else
      5)

### Arguments

`grl` | a `GRangesList` object with usually new ORFs, but can also be either leaders, cds', 3'UTRs.
`tx` | a GrangesList of transcripts covering grl.
`footprints` | ribo seq reads as GAlignment, GRanges or GRangesList object.
`onlyProportion` | a logical (FALSE), return whole data.frame or only proportions
`average` | a logical (FALSE), take average over coverage in all grl ?
`pShifted` | a logical (TRUE), are riboseq reads p-shifted?
`keep.names` | a logical(FALSE), only applies when onlyProportion is TRUE.
`upStart` | upstream region boundary (5 or 20 as standard), relative (5, mean 5 upstream from TIS)
`downStop` | downstream region boundary (5 or 20 as standard), relative (5, mean 5 downstream from TIS)

### Details

This pattern can be averaged on CDS's, to find other ORFs. When detecting new ORFs, this CDS average can be used as a template.

### Value

a data.frame with lengths by coverage / vector of proportions

[Package ORFik version 1.2.1 Index]