MARVEL (version 1.4.0)

ComputePSI: Compute percent spliced-in (PSI) values

Description

Validate splicing events and subsequently computes percent spliced-in (PSI) values these high-quality splicing events. This is a wrapper function for ComputePSI.SE, ComputePSI.MXE, ComputePSI.A5SS, ComputePSI.A3SS, ComputePSI.RI, ComputePSI.AFE, and ComputePSI.ALE functions.

Usage

ComputePSI(
  MarvelObject,
  CoverageThreshold,
  EventType,
  thread = NULL,
  UnevenCoverageMultiplier = 10,
  read.length = 1
)

Value

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

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.

EventType

Character string. Indicate which splicing event type to calculate the PSI values for. Can take value "SE", "MXE", "RI", "A5SS", or "A3SS" which represents skipped-exon (SE), mutually-exclusive exons (MXE), retained-intron (RI), alternative 5' splice site (A5SS), and alternative 3' splice site (A3SS), respectively.

thread

Numeric value. Only applicable when EventType set to "RI" Set number of threads..

UnevenCoverageMultiplier

Numeric value. Maximum allowable fold difference between two included junction counts for SE or two included or two excluded junction counts for MXE. Only applicable when EventType set to "SE" or "MXE", respectively.

read.length

Numeric value. The length of read.Only applicable when EventType set to "RI". This number will be specific to the sequencing mode. E.g. read length should be set to 150 when samples were sequenced in 150bp paired-end or single-end. This option should only be specified when users used read-counting approach for computing intron counts. The option should be left with its default value 1 when users tabulated the per-base count and summed them up to arrive at the intron counts.

Examples

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

marvel.demo <- ComputePSI(MarvelObject=marvel.demo,
                          CoverageThreshold=10,
                          EventType="SE",
                          UnevenCoverageMultiplier=10
                          )