filterPSI: Filter alternative splicing quantification

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

Description

Filter alternative splicing quantification

Usage

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

# 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.