MARVEL (version 1.4.0)

FilterGenes.10x: Filter specific gene types

Description

Retain genes of specific type, e.g., protein-coding genes.

Usage

FilterGenes.10x(MarvelObject, gene.type = "protein_coding")

Value

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

Arguments

MarvelObject

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

gene.type

Character string. Gene type to keep. Specification should match that of GTF.

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)

# Subset CDS genes
marvel.demo.10x <- FilterGenes.10x(MarvelObject=marvel.demo.10x,
                          gene.type="protein_coding"
                          )