prepareAnnotationFromEvents {psichomics} | R Documentation |
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).
prepareAnnotationFromEvents(...)
... |
Data frame(s) of alternative splicing events to include in the annotation |
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
List of data frames with the annotation from different data frames joined by event type
When cross-referencing events, gene information is discarded.
# 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)