quantifySplicing: Quantify alternative splicing events

In psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

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: discard alternative splicing quantified using a number of reads below this threshold
genes	Character: gene symbols for which the splicing quantification of associated splicing events is performed (by default, splicing events from all genes are selected)

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"))

psichomics documentation built on Nov. 8, 2020, 5:44 p.m.