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

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 1.8.2 Index]