CheckAlignment.10x {MARVEL}

Pre-flight check

Description

Ensures only overlapping cells found in both gene and splice junction data are retained. Also ensures matrix columns matches cell IDs in sample metadata and matrix rows matches gene name or splice junction coordinates in feature metadata.

Usage

CheckAlignment.10x(MarvelObject)

Arguments

MarvelObject

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

Value

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

# 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"
                          )

# Pre-flight check
marvel.demo.10x <- CheckAlignment.10x(MarvelObject=marvel.demo.10x)