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]