create_centroids: Create Centroids

In GSgalgoR: An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer

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)

GSgalgoR documentation built on Nov. 8, 2020, 6:57 p.m.