MARVEL (version 1.4.0)

ValidateSJ.10x: Validate splice junctions

Description

Retains splice junctions whose start and end belong to the same gene.

Usage

ValidateSJ.10x(MarvelObject, keep.novel.sj = FALSE)

Value

An object of class S3 containing the updated slots MarvelObject$sj.metadata and MarvelObject$sj.count.matrix.

Arguments

MarvelObject

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

keep.novel.sj

Logical value. If set to TRUE, novel splice junctions will be retained for downstream analysis. Novel splice junctions are defined as splice junctions with one end reported in GTF while the other was not reported in GTF. Default value is FALSE.

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)

# Validate junctions
marvel.demo.10x <- ValidateSJ.10x(MarvelObject=marvel.demo.10x)