to_dataframe {GSgalgoR} | R Documentation

## Convert galgo.Obj to data.frame

### 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, mguerrero@mendoza-conicet.gob.ar

### 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)

[Package GSgalgoR version 1.4.0 Index]