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 )
output | @param output An object of class |
---|---|
solution.names | A |
train.set | a |
distancetype | a |
usegpu |
|
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
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) }