Description Usage Arguments Value Examples
View source: R/results_functions.R
This functions create the signature centroids estimated from the GalgoR output and the expression matrix of the training sets.
1 2 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## Not run:
# 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)
## End(Not run)
|
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