quantifySplicing {psichomics}

R Documentation

Quantify alternative splicing events

Description

Quantify alternative splicing events

Usage

quantifySplicing(
  annotation,
  junctionQuant,
  eventType = c("SE", "MXE", "ALE", "AFE", "A3SS", "A5SS"),
  minReads = 10,
  genes = NULL
)

Arguments

annotation	List of data frames: annotation for each alternative splicing event type
junctionQuant	Data frame: junction quantification
eventType	Character: splicing event types to quantify
minReads	Integer: values whose number of total supporting read counts is below minReads are returned as NA
genes	Character: gene symbols for which to quantify splicing events (if NULL, events from all genes are quantified)

Value

Data frame with the quantification of the alternative splicing events

See Also

Other functions for PSI quantification: filterPSI(), getSplicingEventTypes(), listSplicingAnnotations(), loadAnnotation(), plotRowStats()

Examples

# Calculate PSI for skipped exon (SE) and mutually exclusive (MXE) events
annot <- readFile("ex_splicing_annotation.RDS")
junctionQuant <- readFile("ex_junctionQuant.RDS")

quantifySplicing(annot, junctionQuant, eventType=c("SE", "MXE"))

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