GWCoGAPS {CoGAPS} | R Documentation

## GWCoGAPS

### Description

GWCoGAPS

### Usage

    GWCoGAPS(simulationName, nFactor, nCores = NA, cut = NA, minNS = NA,
      manualMatch = FALSE, consensusPatterns = NULL,
      saveUnmatchedPatterns = FALSE, ...)

### Arguments

`simulationName` | name of this simulation
`nFactor` | number of patterns (basis vectors, metagenes), which must be greater than or equal to the number of rows of FP
`nCores` | number of cores for parallelization. If left to the default NA, nCores = nSets.
`cut` | number of branches at which to cut dendrogram used in patternMatch4Parallel
`minNS` | minimum of individual set contributions a cluster must contain
`manualMatch` | logical indicating whether or not to stop after initial phase for manual pattern matching
`consensusPatterns` | fixed pattern matrix to be used to ensure reciprocity of A weights accross sets
`saveUnmatchedPatterns` | option to save intermediate results for each set, before the pattern matching happens
`...` | additional parameters to be fed into `gapsRun` and `gapsMapRun`

### Details

calls the C++ MCMC code and performs Bayesian matrix factorization returning the two matrices that reconstruct the data matrix for whole genome data;

### Value

list of A and P estimates

### See Also

`gapsRun`, `patternMatch4Parallel`, and `gapsMapRun`

### Examples

    data(SimpSim)
    sim_name <- "example"
    createGWCoGAPSSets(SimpSim.D, SimpSim.S, nSets=2, sim_name)
    result <- GWCoGAPS(sim_name, nFactor=3, nEquil=200, nSample=200)

[Package CoGAPS version 3.0.2 Index]