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

View source: R/cage_annotations.R

addNewTSSOnLeadersR Documentation

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


Roleren/ORFik documentation built on Oct. 19, 2024, 7:37 a.m.