getSampleFromSubject: Get samples matching the given subjects

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

Description

Get samples matching the given subjects

Usage

getSampleFromSubject(
  patients,
  samples,
  clinical = NULL,
  rm.NA = TRUE,
  match = NULL,
  showMatch = FALSE
)

Arguments

patients	Character or list of characters: subject identifiers
samples	Character: sample identifiers
clinical	Data frame or matrix: clinical dataset
rm.NA	Boolean: remove missing values?
match	Integer: vector of subject index with the sample identifiers as name to save time (optional)
showMatch	Boolean: show matching subject index?

Value

Names of the matching samples (if showMatch = TRUE, a character with the subjects as values and their respective samples as names is returned)

See Also

Other functions for data grouping: createGroupByAttribute(), getGeneList(), getSubjectFromSample(), groupPerElem(), plotGroupIndependence(), testGroupIndependence()

Examples

subjects <- c("GTEX-ABC", "GTEX-DEF", "GTEX-GHI", "GTEX-JKL", "GTEX-MNO")
samples <- paste0(subjects, "-sample")
clinical <- data.frame(samples=samples)
rownames(clinical) <- subjects
getSampleFromSubject(subjects[c(1, 4)], samples, clinical)

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