addNewTSSOnLeaders: Add cage max peaks as new transcript start sites for each 5'...

In JokingHero/ORFik: Open Reading Frames in Genomics

Add cage max peaks as new transcript start sites for each 5' leader (*) strands are not supported, since direction must be known.

Description

Add cage max peaks as new transcript start sites for each 5' leader (*) strands are not supported, since direction must be known.

Usage

addNewTSSOnLeaders(fiveUTRs, maxPeakPosition, removeUnused, cageMcol)

Arguments

fiveUTRs	(GRangesList) The 5' leaders or full transcript sequences
maxPeakPosition	The max peak for each 5' leader found by cage
removeUnused	logical (FALSE), if False: (standard is to set them to original annotation), If TRUE: remove leaders that did not have any cage support.
cageMcol	a logical (FALSE), if TRUE, add a meta column to the returned object with the raw CAGE counts in support for new TSS.

Value

a GRanges object of first exons

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.