toList: Convert galgo.Obj to list

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

Description

The current function transforms a galgo.Obj to a list

Usage

toList(output)

Arguments

output

An object of class galgo.Obj

Value

The current function restructurates a galgo.Obj to a more easy to understand an use list. This output is particularly useful if one wants to select a given solution and use its outputs in a new classifier. The output of type list has a length equals to the number of solutions obtained by the galgo algorithm.

Basically this output is a list of lists, where each element of the output is named after the solution's name (solution.n, where n is the number assigned to that solution), and inside of it, it has all the constituents for that given solution with the following structure:

1. output$solution.n$Genes: A vector of the features included in the solution

2. output$solution.n$k: The number of partitions found in that solution

3. output$solution.n$SC.Fit: The average silhouette coefficient of the partitions found

4. output$solution.n$Surv.Fit: The survival fitness value

5. output$solution.n$Rank: The solution rank

6. CrowD: The solution crowding distance related to the rest of the solutions

Author(s)

Martin E Guerrero-Gimenez, [e-mail]

Examples

## 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)
outputList <- toList(output)

## End(Not run)

harpomaxx/galgo documentation built on Aug. 11, 2020, 3:07 p.m.