FilterGenes.10x: Filter specific gene types

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Filter specific gene types

Description

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

Usage

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

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.

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.

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"
                          )

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