CheckAlignment {MARVEL}

Pre-flight check

Description

Checks if the metadata aligns with the columns and rows of the matrix for splicing or gene data. This is a wrapper function for CheckAlignment.PSI, CheckAlignment.Exp, CheckAlignment.PSI.Exp, and CheckAlignment.SJ.

Usage

CheckAlignment(MarvelObject, level)

Arguments

MarvelObject

Marvel object. S3 object generated from CreateMarvelObject function.

level

Character string. Indicate "SJ", "splicing" or "gene" for splice junction, splicing or gene data, respectively. "SJ" typically specified before computing PSI values. "splicing" or "gene" typically specified after computing PSI values.

Value

An object of class S3 with updated slots MarvelObject$SpliceJunction, MarvelObject$IntronCoverage, MarvelObject$SplicePheno, MarvelObject$SpliceFeatureValidated, and MarvelObject$PSI or MarvelObject$GenePheno, MarvelObject$GeneFeature, and MarvelObject$Gene are updated for splicing or gene data, respectively.

Examples

marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))

marvel.demo <- CheckAlignment(MarvelObject=marvel.demo,
                              level="SJ"
                              )