filterPSI: Filter alternative splicing quantification

Description Usage Arguments Value See Also Examples

View source: R/data_inclusionLevelsFilter.R

Description

Filter alternative splicing quantification

Usage

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filterPSI(
  psi,
  eventType = NULL,
  eventSubtype = NULL,
  minPSI = -Inf,
  maxPSI = Inf,
  minMedian = -Inf,
  maxMedian = Inf,
  minLogVar = -Inf,
  maxLogVar = Inf,
  minRange = -Inf,
  maxRange = Inf
)

Arguments

psi

Data frame or matrix: alternative splicing quantification

eventType

Character: filter data based on event type; check all event types available by using getSplicingEventTypes(psi), where psi is the alternative splicing quantification data; if eventType = NULL, events are not filtered by event type

eventSubtype

Character: filter data based on event subtype; check all event subtypes available in your data by using unique(getSplicingEventData(psi)$subtype), where psi is the alternative splicing quantification data; if eventSubtype = NULL, events are not filtered by event subtype

minPSI

Numeric: minimum PSI value

maxPSI

Numeric: maximum PSI value

minMedian

Numeric: minimum median PSI per splicing event

maxMedian

Numeric: maximum median PSI per splicing event

minLogVar

Numeric: minimum log10(PSI variance) per splicing event

maxLogVar

Numeric: maximum log10(PSI variance) per splicing event

minRange

Numeric: minimum PSI range across samples per splicing event

maxRange

Numeric: maximum PSI range across samples per splicing event

Value

Boolean vector indicating which splicing events pass the thresholds

See Also

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

Examples

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

psi <- quantifySplicing(annot, junctionQuant, eventType=c("SE", "MXE"))
# Filter PSI
psi[filterPSI(psi, minMedian=0.05, maxMedian=0.95, minRange=0.15), ]

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