filterPSI {psichomics}R Documentation

Filter alternative splicing quantification

Description

Filter alternative splicing quantification

Usage

filterPSI(
  psi,
  minMedian = -Inf,
  maxMedian = Inf,
  minLogVar = -Inf,
  maxLogVar = Inf,
  minRange = -Inf,
  maxRange = Inf
)

Arguments

psi

Data frame or matrix: alternative splicing quantification

minMedian

Numeric: minimum of read count median per splicing event

maxMedian

Numeric: maximum of read count median per splicing event

minLogVar

Numeric: minimum log10(read count variance) per splicing event

maxLogVar

Numeric: maximum log10(read count variance) per splicing event

minRange

Numeric: minimum range of read counts across samples per splicing event

maxRange

Numeric: maximum range of read counts 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"))
psi[filterPSI(psi, minMedian=0.05, maxMedian=0.95, minRange=0.15), ]
[Package psichomics version 1.12.1 Index]