Parse events from alternative splicing annotation

Parse events from alternative splicing annotation

Usage

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
)

Arguments

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, hg19; depends on the program of origin)

complexEvents

Boolean: should complex events in A3SS and A5SS be parsed?

novelEvents

Boolean: parse events detected due to novel splice sites

Value

Retrieve data frame with events based on a given alternative splicing annotation

Details

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

See also

Other functions to prepare alternative splicing annotations: prepareAnnotationFromEvents()

Examples

# Load sample files
folder <- "extdata/eventsAnnotSample/suppa_output/suppaEvents"
suppaOutput <- system.file(folder, package="psichomics")

suppa <- parseSuppaAnnotation(suppaOutput)
#> 
#> Retrieving SUPPA annotation...
#> 
#> Parsing SUPPA annotation...
# Load sample files
folder <- "extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES"
vastToolsOutput <- system.file(folder, package="psichomics")

vast <- parseVastToolsAnnotation(vastToolsOutput)
#> 
#> Retrieving VAST-TOOLS annotation...
#> 
#> Parsing VAST-TOOLS annotation...
#> 
#> ALT3
#> 
#> ALT5
#> 
#> COMBI
#> 
#> EXSK
#> 
#> IR
#> 
#> MERGE3m
#> 
#> MIC
#> 
#> MULTI
# Load sample files
folder <- "extdata/eventsAnnotSample/miso_annotation"
misoOutput <- system.file(folder, package="psichomics")

miso <- parseMisoAnnotation(misoOutput)
#> 
#> Retrieving MISO annotation...
#> 
#> Parsing MISO annotation...
# Load sample files
folder <- "extdata/eventsAnnotSample/mats_output/ASEvents"
matsOutput <- system.file(folder, package="psichomics")

mats <- parseMatsAnnotation(matsOutput)
#> 
#> Retrieving rMATS annotation...
#> 
#> Parsing rMATS annotation...

# Do not parse novel events
mats <- parseMatsAnnotation(matsOutput, novelEvents=FALSE)
#> 
#> Retrieving rMATS annotation...
#> 
#> Parsing rMATS annotation...