parseMisoAnnotation: Get events from alternative splicing annotation

Description Usage Arguments Details Value Examples

View source: R/events_miso.R

Description

Get events from alternative splicing annotation

Usage

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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? FALSE by default

novelEvents

Boolean: parse events dedected due to novel splice sites (TRUE by default)

Details

Type of parsable events:

Value

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

Examples

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# 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)

nuno-agostinho/psichomics documentation built on Nov. 1, 2017, 3:18 p.m.