parseMatsEvent: Parse alternative splicing events from MATS

In psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Description

Parse alternative splicing events from MATS

Usage

parseMatsEvent(event, event_type)

Arguments

event	Data frame row: MATS splicing event
event_type	Character: Type of event to parse (see details)

Details

The following event types can be parsed:

• SE: Skipped exon

• MXE: Mutually exclusive exons

• RI:Retained intron

• A3SS: Alternative 3' splice site

• A5SS: Alternative 5' splice site

Value

List containing the event attributes and junctions

Examples

# MATS event (alternative 3' splice site)
event <- read.table(text = "
     2 ENSG00000166012 TAF1D chr11 - 93466515 93466671 93466515 93466563 93467790 93467826
     5 ENSG00000166012 TAF1D chr11 - 93466515 93466671 93466515 93466585 93467790 93467826
     6 ENSG00000166012 TAF1D chr11 - 93466515 93466585 93466515 93466563 93467790 93467826
")
psichomics:::parseMatsEvent(event, "A3SS")

psichomics documentation built on Nov. 8, 2020, 5:44 p.m.