MARVEL (version 1.4.0)

SubsetCrypticA3SS: Differential gene expression analysis for differentially spliced genes

Description

Performs differential gene expression analysis between 2 groups of cells only on differentially spliced genes.

Usage

SubsetCrypticA3SS(MarvelObject, method, distance.to.ss = c(1, 100))

Value

An object of class S3 updated slot MarvelObject$DE$PSI$Table and new slot MarvelObject$DE$PSI$A3SS.dist.to.ss.

Arguments

MarvelObject

Marvel object. S3 object generated from TransformExpValues function.

method

Vector of character string(s). To include splicing events from these method(s) for differential splicing analysis.

distance.to.ss

Character string. Range of distances between A3SS and canonical splice site to consider A3SS to be cryptic. Default value c(1, 100).

Examples

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

marvel.demo <- SubsetCrypticA3SS(MarvelObject=marvel.demo,
                                 method="ad",
                                 distance.to.ss=c(1,100)
                                 )

# Check output
head(marvel.demo$DE$PSI$Table[["ad"]])