# genAlgConsensus: Find Edges Separating Two Groups using Multiple Genetic... In bingat: Binary Graph Analysis Tools

## Description

GA-Mantel is a fully multivariate method that uses a genetic algorithm to search over possible edge subsets using the Mantel correlation as the scoring measure for assessing the quality of any given edge subset.

## Usage

 ```1 2``` ``` genAlgConsensus(data, covars, consensus = .5, numRuns = 10, parallel = FALSE, cores = 3, ...) ```

## Arguments

 `data` A matrix of edges(rows) for each sample(columns). `covars` A matrix of covariates(columns) for each sample(rows). `consensus` The required fraction (0, 1] of solutions containing an edge in order to keep it. `numRuns` Number of runs to do. In practice the number of runs needed varies based on data set size and the GA parameters set. `parallel` When this is 'TRUE' it allows for parallel calculation of the bootstraps. Requires the package `doParallel`. `cores` The number of parallel processes to run if parallel is 'TRUE'. `...` Other arguments for the GA function see genAlg

## Details

Use a GA consensus approach to find edges that separate subjects based on group membership or set of covariates if you cannot run the GA long enough to get a final solution.

## Value

A list containing

 `solutions` The best solution from each run. `consSol` The consensus solution. `selectedIndex` The selected edges by row number.

## Author(s)

Sharina Carter, Elena Deych, Berkley Shands, William D. Shannon

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19``` ``` ## Not run: data(braingraphs) ### Set covars to just be group membership covars <- matrix(c(rep(0, 19), rep(1, 19))) ### We use low numbers for speed. The exact numbers to use depend ### on the data being used, but generally the higher iters and popSize ### the longer it will take to run. earlyStop is then used to stop the ### run early if the results aren't improving. iters <- 500 popSize <- 200 earlyStop <- 250 numRuns <- 3 gaRes <- genAlgConsensus(braingraphs, covars, .5, numRuns, FALSE, 3, iters, popSize, earlyStop) ## End(Not run) ```

bingat documentation built on May 1, 2019, 9:11 p.m.