to_dataframe: Convert galgo.Obj to data.frame

In harpomaxx/galgoR-package: 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

to_dataframe(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

# 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)

harpomaxx/galgoR-package documentation built on Oct. 26, 2020, 7:05 a.m.