prepareAnnotationFromEvents: Prepare annotation from alternative splicing events

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

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.

See Also

Other functions to prepare alternative splicing annotations: parseSuppaAnnotation()

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)

nuno-agostinho/psichomics documentation built on Feb. 11, 2024, 11:16 p.m.