create_centroids {GSgalgoR} | R Documentation |
This functions create the signature centroids estimated from the GalgoR output and the expression matrix of the training sets.
create_centroids (output, solution_names, trainset, distancetype = "pearson")
output |
@param output An object of class |
solution_names |
A |
trainset |
a |
distancetype |
a |
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
# load example dataset library(breastCancerTRANSBIG) data(transbig) Train <- transbig rm(transbig) expression <- Biobase::exprs(Train) clinical <- Biobase::pData(Train) OS <- survival::Surv(time = clinical$t.rfs, event = clinical$e.rfs) # We will use a reduced dataset for the example expression <- expression[sample(1:nrow(expression), 100), ] # Now we scale the expression matrix expression <- t(scale(t(expression))) # Run galgo output <- GSgalgoR::galgo(generations = 5, population = 15, prob_matrix = expression, OS = OS) outputDF <- to_dataframe(output) outputList <- to_list(output) RESULTS <- non_dominated_summary( output = output, OS = OS, prob_matrix = expression, distancetype = "pearson" ) CentroidsList <- create_centroids(output, RESULTS$solution, trainset = expression)