create_centroids {GSgalgoR}

R Documentation

Create Centroids

Description

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

Usage

create_centroids (output, solution_names, trainset,
distancetype = "pearson")

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
trainset	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'

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

# 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)

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