prepareAnnotationFromEvents {psichomics} | R Documentation

## Prepare annotation from alternative splicing events

### Description

In case more than one data frame with alternative splicing events is given, the events are cross-referenced according to the chromosome, strand and relevant coordinates per event type (see details).

### Usage

    prepareAnnotationFromEvents(...)

### Arguments

`...` | Data frame(s) of alternative splicing events to include in the annotation

### Details

Events from two or more data frames are cross-referenced based on each event's chromosome, strand and specific coordinates relevant for each event type:

- Skipped exon: constitutive exon 1 end, alternative exon (start and end) and constitutive exon 2 start

- Mutually exclusive exon: constitutive exon 1 end, alternative exon 1 and 2 (start and end) and constitutive exon 2 start

- Alternative 5' splice site: constitutive exon 1 end, alternative exon 1 end and constitutive exon 2 start

- Alternative first exon: same as alternative 5' splice site

- Alternative 3' splice site: constitutive exon 1 end, alternative exon 1 start and constitutive exon 2 start

- Alternative last exon: same as alternative 3' splice site

### Value

List of data frames with the annotation from different data frames joined by event type

### Note

When cross-referencing events, gene information is discarded.

### Examples

    # Load sample files (SUPPA annotation)
    folder <- "extdata/eventsAnnotSample/suppa_output/suppaEvents"
    suppaOutput <- system.file(folder, package="psichomics")

    # Parse and prepare SUPPA annotation
    suppa <- parseSuppaAnnotation(suppaOutput)
    annot <- prepareAnnotationFromEvents(suppa)

    # Load sample files (rMATS annotation)
    folder <- "extdata/eventsAnnotSample/mats_output/ASEvents/"
    matsOutput <- system.file(folder, package="psichomics")

    # Parse rMATS annotation and prepare combined annotation from rMATS and SUPPA
    mats <- parseMatsAnnotation(matsOutput)
    annot <- prepareAnnotationFromEvents(suppa, mats)

[Package psichomics version 1.8.2 Index]