to_dataframe {GSgalgoR} | R Documentation |
The current function transforms a galgo.Obj
to a data.frame
to_dataframe(output)
output |
An object of class |
The current function restructurates a galgo.Obj
to a more
easy to understand an use data.frame
. The output data.frame
has m x n dimensions, were the rownames (m) are the solutions
obtained by the galgo
algorithm.
The columns has the following structure:
Genes: The features included in each solution in form
of a list
k: The number of partitions found in that solution
SC.Fit: The average silhouette coefficient of the partitions found
Surv.Fit: The survival fitness value
Rank: The solution rank
CrowD: The solution crowding distance related to the rest of the solutions
Martin E Guerrero-Gimenez, mguerrero@mendoza-conicet.gob.ar
# 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)