assignValuePerSubject: Assign average sample values to their corresponding subjects

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Assign average sample values to their corresponding subjects

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)

nuno-agostinho/psichomics documentation built on Feb. 11, 2024, 11:16 p.m.