ParseGTF: Parse gene transfer file (GTF)

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Parse gene transfer file (GTF)

Description

Parses the gene transfer file (GTF) for downstream nonsense-mediated decay (NMD) prediction.

Usage

ParseGTF(MarvelObject)

Arguments

MarvelObject

Marvel object. S3 object generated from CompareValues.PSI function.

Details

This function parses the GTF in order to generate new columns for gene IDs, transcript IDs, and transcript type. These information are extracted from the attribute (9th) column for a standard GTF. These information will be used for downstream NMD prediction.

Value

An object of class S3 with new slot MarvelObject$NMD$GTF.

Examples

marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))

marvel.demo <- ParseGTF(MarvelObject=marvel.demo)

MARVEL documentation built on Oct. 31, 2022, 5:07 p.m.