Prepare annotation from alternative splicing events — prepareAnnotationFromEvents • psichomics

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

Value

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

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

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)
#> 
#> Retrieving SUPPA annotation...
#> 
#> Parsing SUPPA annotation...
annot <- prepareAnnotationFromEvents(suppa)
#> 
#> Sorting coordinates...
#> 
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#> Joining events per event type...
#> 
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#> Cleaning the annotation...

# 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)
#> 
#> Retrieving rMATS annotation...
#> 
#> Parsing rMATS annotation...
annot <- prepareAnnotationFromEvents(suppa, mats)
#> 
#> Sorting coordinates...
#> 
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#> Joining events per event type...
#> 
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#> Cleaning the annotation...