Create Centroids — create_centroids • galgoR

This functions create the signature centroids estimated from the GalgoR output and the expression matrix of the training sets.

create_centroids(
  output,
  solution.names,
  train.set,
  distancetype = "pearson",
  usegpu = FALSE
)

Arguments

output	@param output An object of class `galgo.Obj`
solution.names	A `character` vector with the names of the solutions for which the centroids are to be calculated
train.set	a `matrix` or `data.frame`. Must be an expression matrix with features in rows and samples in columns
distancetype	a `character` that can be either `'pearson'`, `'uncentered'`, `'spearman'` or `'euclidean'`
usegpu	`logical` `TRUE` or `FALSE`

Value

Returns a list with the centroid matrix for each of the solutions in solution.names, where each column represents the prototypic centroid of a subtype and each row the constituents features of the solution signature

Examples

if (FALSE) {
# Load data
rna_luad <- use_rna_luad()
TCGA_expr <- rna_luad$TCGA$expression_matrix
TCGA_clinic <- rna_luad$TCGA$pheno_data
OS <- survival::Surv(time = TCGA_clinic$time, event = TCGA_clinic$status)

# Run galgo
output <- galgoR::galgo(generations = 10, population = 30, prob_matrix = TCGA_expr, OS = OS)
RESULTS <- non_dominated_summary(
  output = output, OS = OS,
  prob_matrix = TCGA_expr,
  distancetype = "pearson",
  usegpu = FALSE
)
CentroidsList <- create_centroids(output, RESULTS$solution, train.set = TCGA_expr)
}