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]