prepareAnnotationFromEvents: Prepare annotation from alternative splicing events

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

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)

Example output

Loading required package: shiny
Loading required package: shinyBS
Start the visual interface by running the function psichomics()
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Retrieving SUPPA annotation...
Parsing SUPPA annotation...
Sorting coordinates...
[1] "A3SS SUPPA"
[1] "A5SS SUPPA"
[1] "AFE SUPPA"
[1] "ALE SUPPA"
[1] "MXE SUPPA"
Joining events per event type...
A3SS
A5SS
AFE
ALE
MXE
RI
SE
Cleaning the annotation...
Retrieving rMATS annotation...
Parsing rMATS annotation...
Sorting coordinates...
[1] "A3SS MATS"
[1] "A3SS SUPPA"
[1] "A5SS MATS"
[1] "A5SS SUPPA"
[1] "AFE MATS"
[1] "AFE SUPPA"
[1] "ALE MATS"
[1] "ALE SUPPA"
[1] "MXE MATS"
[1] "MXE SUPPA"
Joining events per event type...
A3SS
A5SS
AFE
ALE
MXE
RI
SE
Cleaning the annotation...

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