getValuePerPatient {psichomics}R Documentation

Assign average sample values to their corresponding patients

Description

Assign average sample values to their corresponding patients

Usage

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

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

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

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

getPSIperPatient(psi, match, clinical = NULL, patients = NULL, ...)

Arguments

data

One-row data frame/matrix or vector: values per sample for a single gene

match

Matrix: match between samples and patients

clinical

Data frame or matrix: clinical dataset (only required if the patients argument is not handed)

patients

Character: patient identifiers (only required if the clinical argument is not handed)

samples

Character: samples to use when assigning values per patient (if NULL, all samples will be used)

psi

Data frame or matrix: values per sample

...

Deprecated arguments

Value

Values per patient

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("Patient", 1:3), 2)
names(match) <- colnames(psi)

assignValuePerSubject(psi[3, ], match)

[Package psichomics version 1.8.2 Index]