AnnotateSJ.10x: Annotate splice junctions
In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

View source: R/Script_DROPLET_02_PREPROCESS_2_AnnotateSJ.R

AnnotateSJ.10x

R Documentation

Annotate splice junctions

Description

Annotates the splice junctions by assigning the gene name to the start and end of the splice junction. Annotations are retrieved from GTF.

Usage

AnnotateSJ.10x(MarvelObject)

Arguments

MarvelObject

Marvel object. S3 object generated from AnnotateGenes.10x function.

Value

An object of class S3 containing the updated slot MarvelObject$sj.metadata.

Examples


# Load un-processed MARVEL object
marvel.demo.10x.raw <- readRDS(system.file("extdata/data",
                               "marvel.demo.10x.raw.rds",
                               package="MARVEL")
                               )

# Annotate gene metadata
marvel.demo.10x <- AnnotateGenes.10x(MarvelObject=marvel.demo.10x.raw)

# Annotate junction metadata
marvel.demo.10x <- AnnotateSJ.10x(MarvelObject=marvel.demo.10x)

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