filterPSI {psichomics} | R Documentation |
Filter alternative splicing quantification
filterPSI( psi, eventType = NULL, eventSubtype = NULL, minPSI = -Inf, maxPSI = Inf, minMedian = -Inf, maxMedian = Inf, minLogVar = -Inf, maxLogVar = Inf, minRange = -Inf, maxRange = Inf )
psi |
Data frame or matrix: alternative splicing quantification |
eventType |
Character: filter data based on event type; check all event
types available by using |
eventSubtype |
Character: filter data based on event subtype; check all
event subtypes available in your data by using
|
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 |
Boolean vector indicating which splicing events pass the thresholds
Other functions for PSI quantification:
getSplicingEventTypes()
,
listSplicingAnnotations()
,
loadAnnotation()
,
plotRowStats()
,
quantifySplicing()
# 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), ]