addCdsOnLeaderEnds: Extends leaders downstream

In JokingHero/ORFik: Open Reading Frames in Genomics

Extends leaders downstream

Description

When finding uORFs, often you want to allow them to end inside the cds.

Usage

addCdsOnLeaderEnds(fiveUTRs, cds, onlyFirstExon = FALSE)

Arguments

fiveUTRs	The 5' leader sequences as GRangesList
cds	If you want to extend 5' leaders downstream, to catch uorfs going into cds, include it.
onlyFirstExon	logical (F), include whole cds or only first exons.

Details

This is a simple way to do that

Value

a GRangesList of cds exons added to ends

See Also

Other uorfs: filterUORFs(), removeORFsWithSameStartAsCDS(), removeORFsWithSameStopAsCDS(), removeORFsWithStartInsideCDS(), removeORFsWithinCDS(), uORFSearchSpace()

JokingHero/ORFik documentation built on April 7, 2024, 2:59 a.m.