MARVEL (version 1.4.0)

ComputePSI.SE: Compute skipped-exon (SE) percent spliced-in (PSI) values

Description

Validate SE splicing events and subsequently computes percent spliced-in (PSI) values these high-quality splicing events.

Usage

ComputePSI.SE(MarvelObject, CoverageThreshold, UnevenCoverageMultiplier = 10)

Value

An object of class S3 with new slots $SpliceFeatureValidated$SE

$PSI$SE.

Arguments

MarvelObject

S3 object generated from CreateMarvelObject 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.

UnevenCoverageMultiplier

Numeric value. Maximum allowable fold difference between two included junction counts.

Details

This function computes the PSI for each SE splicing event. Splicing events provided in SpliceFeature data frame will first be cross-checked against the splice junctions provided in SpliceJunction data frame. Only events whose junctions are found in SpliceJunction are retained. The formula for computing PSI is the number of junction reads supporting the included isoform divided by 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.SE(MarvelObject=marvel.demo,
                             CoverageThreshold=10,
                             UnevenCoverageMultiplier=10
                             )