assignValuePerSubject: Assign average sample values to their corresponding subjects

In psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Description

Assign average sample values to their corresponding subjects

Usage

assignValuePerSubject(
  data,
  match,
  clinical = NULL,
  patients = NULL,
  samples = NULL
)

Arguments

data	One-row data frame/matrix or vector: values per sample for a single gene
match	Matrix: match between samples and subjects
clinical	Data frame or matrix: clinical dataset (only required if the subjects argument is not handed)
patients	Character: subject identifiers (only required if the clinical argument is not handed)
samples	Character: samples to use when assigning values per subject (if NULL, all samples will be used)

Value

Values per subject

See Also

Other functions to analyse survival: getAttributesTime(), labelBasedOnCutoff(), optimalSurvivalCutoff(), plotSurvivalCurves(), plotSurvivalPvaluesByCutoff(), processSurvTerms(), survdiffTerms(), survfit.survTerms(), testSurvival()

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"))

# Match between subjects and samples
match <- rep(paste("Subject", 1:3), 2)
names(match) <- colnames(psi)

# Assign PSI values to each subject based on the PSI of their samples
assignValuePerSubject(psi[3, ], match)

psichomics documentation built on Nov. 8, 2020, 5:44 p.m.