parseSuppaAnnotation {psichomics} | R Documentation |
Parse events from alternative splicing annotation
parseSuppaAnnotation( folder, types = c("SE", "AF", "AL", "MX", "A5", "A3", "RI"), genome = "hg19" ) parseVastToolsAnnotation( folder, types = c("ALT3", "ALT5", "COMBI", "IR", "MERGE3m", "MIC", "EXSK", "MULTI"), genome = "Hsa", complexEvents = FALSE ) parseMisoAnnotation( folder, types = c("SE", "AFE", "ALE", "MXE", "A5SS", "A3SS", "RI", "TandemUTR"), genome = "hg19" ) parseMatsAnnotation( folder, types = c("SE", "AFE", "ALE", "MXE", "A5SS", "A3SS", "RI"), genome = "fromGTF", novelEvents = TRUE )
folder |
Character: path to folder |
types |
Character: type of events to retrieve (depends on the program of origin; see details) |
genome |
Character: genome of interest (for instance, |
complexEvents |
Boolean: should complex events in A3SS and A5SS be parsed? |
novelEvents |
Boolean: parse events detected due to novel splice sites |
Type of parsable events:
Alternative 3' splice site
Alternative 5' splice site
Alternative first exon
Alternative last exon
Skipped exon (may include skipped micro-exons)
Mutually exclusive exon
Retained intron
Tandem UTR
Retrieve data frame with events based on a given alternative splicing annotation
Other functions to prepare alternative splicing annotations:
prepareAnnotationFromEvents()
# Load sample files folder <- "extdata/eventsAnnotSample/suppa_output/suppaEvents" suppaOutput <- system.file(folder, package="psichomics") suppa <- parseSuppaAnnotation(suppaOutput) # Load sample files folder <- "extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES" vastToolsOutput <- system.file(folder, package="psichomics") vast <- parseVastToolsAnnotation(vastToolsOutput) # Load sample files folder <- "extdata/eventsAnnotSample/miso_annotation" misoOutput <- system.file(folder, package="psichomics") miso <- parseMisoAnnotation(misoOutput) # Load sample files folder <- "extdata/eventsAnnotSample/mats_output/ASEvents" matsOutput <- system.file(folder, package="psichomics") mats <- parseMatsAnnotation(matsOutput) # Do not parse novel events mats <- parseMatsAnnotation(matsOutput, novelEvents=FALSE)