filterPSI {psichomics} | R Documentation |
Filter alternative splicing quantification
filterPSI(psi, minMedian = -Inf, maxMedian = Inf, minLogVar = -Inf, maxLogVar = Inf, minRange = -Inf, maxRange = Inf)
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 |
Boolean vector indicating which splicing events pass the thresholds
# 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), ]