MARVEL (version 1.4.0)

ModalityChange: Classify modality changes

Description

Classifies the type of modality change for each splicing event that has taken place between 2 groups of cells.

Usage

ModalityChange(MarvelObject, method, psi.pval, psi.delta = 0)

Value

An object of class S3 with new slots MarvelObject$DE$Modality$Table, MarvelObject$DE$Modality$Plot, and MarvelObject$DE$Modality$Plot.Stats.

Arguments

MarvelObject

Marvel object. S3 object generated from CompareValues function.

method

Character string. The statistical method used for differential splicing analysis.

psi.pval

Numeric value. Adjusted p-value below which the splicing event is considered differentially spliced and included for modality analysis.

psi.delta

Numeric value. The absolute difference between the means PSI values of cell group 1 and 2, above which, the splicing event is considered differentially spliced and included for modality analysis.

Examples

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

marvel.demo <- ModalityChange(MarvelObject=marvel.demo,
                              method="ad",
                              psi.pval=0.1,
                              psi.delta=0
                              )

# Check outputs
head(marvel.demo$DE$Modality$Table)
marvel.demo$DE$Modality$Plot
marvel.demo$DE$Modality$Plot.Stats