parseSuppaAnnotation {psichomics} | R Documentation

## Parse events from alternative splicing annotation

### Description

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

### 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

### Value

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

### 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)
    # 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)

[Package psichomics version 1.16.0 Index]