filterPSI {psichomics} | R Documentation

## Filter alternative splicing quantification

### 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), ]

[Package psichomics version 1.20.2 Index]