Description Usage Arguments Details Value Author(s) Examples

View source: R/genAlgConsensus.R

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.

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

`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 |

`cores` |
The number of parallel processes to run if parallel is 'TRUE'. |

`...` |
Other arguments for the GA function see genAlg |

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.

A list containing

`solutions` |
The best solution from each run. |

`consSol` |
The consensus solution. |

`selectedIndex` |
The selected edges by row number. |

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

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)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.