psichomics quantifies alternative splicing based on alternative splicing event annotations from MISO, SUPPA, VAST-TOOLS and rMATS. New alternative splicing annotation may be prepared and used in psichomics by parsing alternative splicing events from those tools. Please contact me if you would like to see support for other tools.
This tutorial will guide you on how to parse alternative splicing events from different tools. To do so, start by loading the following packages:
SUPPA generates alternative splicing events based on a transcript
annotation. Start by running SUPPA's
generateEvents script with a transcript
file (GTF format) for all event types, if desired. See SUPPA's page for
The resulting output will include a directory containing tab-delimited files
with alternative splicing events (one file for each event type). Hand the path
of this directory to the function
parseSuppaAnnotation(), prepare the
prepareAnnotationFromEvents() and save the output to a RDS
suppaOutput <- system.file("extdata/eventsAnnotSample/suppa_output/suppaEvents", package="psichomics") suppaFile <- tempfile(fileext=".RDS")
# suppaOutput <- "path/to/SUPPA/output" # Replace `genome` for the string with the identifier before the first # underscore in the filenames of that directory (for instance, if one of your # filenames of interest is "hg19_A3.ioe", the string would be "hg19") suppa <- parseSuppaAnnotation(suppaOutput, genome="hg19") annot <- prepareAnnotationFromEvents(suppa) # suppaFile <- "suppa_hg19_annotation.RDS" saveRDS(annot, file=suppaFile)
Just like SUPPA, rMATS also allows to generate alternative splicing events based on a transcript annotation, although two BAM or FASTQ files are required to generate alternative splicing events. Read rMATS' page for more information.
The resulting output of rMATS is then handed out to the function
matsOutput <- system.file("extdata/eventsAnnotSample/mats_output/ASEvents/", package="psichomics") matsFile <- tempfile("mats", fileext=".RDS")
# matsOutput <- "path/to/rMATS/output" mats <- parseMatsAnnotation( matsOutput, # Output directory from rMATS genome = "fromGTF", # Identifier of the filenames novelEvents=TRUE) # Parse novel events? annot <- prepareAnnotationFromEvents(mats) # matsFile <- "mats_hg19_annotation.RDS" saveRDS(annot, file=matsFile)
Simply retrieve MISO's alternative splicing annotation and give the path to the downloaded folder as input.
misoAnnotation <- system.file("extdata/eventsAnnotSample/miso_annotation", package="psichomics") misoFile <- tempfile("miso", fileext=".RDS")
# misoAnnotation <- "path/to/MISO/annotation" miso <- parseMisoAnnotation(misoAnnotation) annot <- prepareAnnotationFromEvents(miso) # misoFile <- "miso_AS_annotation_hg19.RDS" saveRDS(annot, file=misoFile)
Download and extract VAST-TOOLS' alternative splicing annotation
and use the path to the
TEMPLATES subfolder as the input of
parseVastToolsAnnotation(). Complex events (i.e. alternative coordinates for
the exon ends) are not currently supported.
vastAnnotation <- system.file("extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/", package="psichomics") vastFile <- tempfile("vast", fileext=".RDS")
# vastAnnotation <- "path/to/VASTDB/libs/TEMPLATES" vast <- parseVastToolsAnnotation(vastAnnotation, genome="Hsa") annot <- prepareAnnotationFromEvents(vast) # vastFile <- "vast_AS_annotation_hg19.RDS" saveRDS(annot, file=vastFile)
To combine the annotation from different sources, provide the parsed annotations
of interest simultaneously to the function
annotFile <- tempfile(fileext=".RDS")
# Combine the annotation from SUPPA, MISO, rMATS and VAST-TOOLS annot <- prepareAnnotationFromEvents(suppa, vast, mats, miso) # annotFile <- "AS_annotation_hg19.RDS" saveRDS(annot, file=annotFile)
The created alternative splicing annotation can be used in psichomics for alternative splicing quantification. To do so, when using the GUI version of psichomics, be sure to select the Load annotation from file... option, click the button that appears below and select the recently created RDS file.
Otherwise, if you are using the CLI version, perform the following steps:
annot <- readRDS(annotFile) # "annotFile" is the path to the annotation file junctionQuant <- readFile("ex_junctionQuant.RDS") # example set psi <- quantifySplicing(annot, junctionQuant)
psi # may have 0 rows because of the small junction quantification set
All feedback on the program, documentation and associated material (including this tutorial) is welcome. Please send any suggestions and comments to:
Nuno Saraiva-Agostinho (firstname.lastname@example.org)
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