ComputePSI.A5SS {MARVEL}

Compute alternative 5' splice site (A5SS) percent spliced-in (PSI) values

Description

Validate A5SS splicing events and subsequently computes percent spliced-in (PSI) values these high-quality splicing events.

Usage

ComputePSI.A5SS(MarvelObject, CoverageThreshold)

Arguments

MarvelObject

Marvel object. 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.

Value

An object of class S3 with new slots $SpliceFeatureValidated$A5SS and $PSI$A5SS.

Examples

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

marvel.demo <- ComputePSI.A5SS(MarvelObject=marvel.demo,
                               CoverageThreshold=10
                               )