assignAnnotations: Overlaps GRanges object with provided annotations.

In ORFik: Open Reading Frames in Genomics

Description

It will return same list of GRanges, but with metdata columns: trainscript_id - id of transcripts that overlap with each ORF gene_id - id of gene that this transcript belongs to isoform - for coding protein alignment in relation to cds on coresponding transcript, for non-coding transcripts alignment in relation to the transcript.

Usage

assignAnnotations(ORFs, con)

Arguments

ORFs	- GRanges or GRangesList object of your ORFs.
con	- Path to gtf file with annotations.

Value

A GRanges object of your ORFs with metadata columns 'gene', 'transcript', isoform' and 'biotype'.

ORFik documentation built on March 27, 2021, 6 p.m.