toDataFrame: Convert galgo.Obj to data.frame

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 data.frame

Usage

toDataFrame(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 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:

1. Genes: The features included in each solution in form of a list

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

3. SC.Fit: The average silhouette coefficient of the partitions found

4. Surv.Fit: The survival fitness value

5. 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)
outputDF <- toDataFrame(output)

## End(Not run)

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