Get a covariate attached to an NG-CHM dataset.

Get a covariate attached to an NG-CHM dataset.

Usage

chmCovariate(dataset, fullname, where)

Arguments

dataset

The NG-CHM dataset to get the covariate from.

fullname

The full name of the covariate to get. If no covariate with that name exists, return NULL.

where

The axis or axes on which to look for the covariate Can be "row", "column", or "both" (default).

Value

A ngchmCovariate or NULL.

See also

ngchmCovariate

chmNewCovariate

chmCovariateBar

Examples

# If the NGCHMDemoData package is installed, use it to create demo usage
if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
  data(TCGA.GBM.Demo, package = "NGCHMDemoData")
  dataset <- chmNewDataset("gbmexpr", "TCGA GBM Expression Data", TCGA.GBM.ExpressionData)
  dataset <- chmAddCovariate(
    dataset, "column",
    chmNewCovariate("TP53 Mutation", TCGA.GBM.TP53MutationData)
  )
  tp53_mutation <- chmCovariate(dataset, "TP53 Mutation")
}
# Small example not requiring NGCHMDemoData
matrix <- matrix(rnorm(100),
  nrow = 10, ncol = 10,
  dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
)
dataset <- chmNewDataset("Demo", "Random Demo Dataset", matrix)
covariate <- setNames(rnorm(10), colnames(matrix))
dataset <- chmAddCovariate(dataset, "column", chmNewCovariate("Random Covariate", covariate))
random_covariate <- chmCovariate(dataset, "Random Covariate")