MARVEL (version 1.4.0)

ComputePSI.AFE: Compute alternative first exon (AFE) percent spliced-in (PSI) values

Description

Computes percent spliced-in (PSI) for alternative first exon (ALE) splicing events.

Usage

ComputePSI.AFE(MarvelObject, CoverageThreshold = 10)

Value

An object of class S3 containing with new slots $SpliceFeatureValidated$AFE and $PSI$AFE.

Arguments

MarvelObject

Marvel object. S3 object generated from DetectEvents function.

CoverageThreshold

Numeric value. Coverage threshold below which the PSI of the splicing event will be censored, i.e. annotated as missing (NA). Coverage defined as the total number of reads supporting both included and excluded isoforms.

Examples

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

marvel.demo <- ComputePSI.AFE(MarvelObject=marvel.demo,
                              CoverageThreshold=10
                              )