GWCoGAPS {CoGAPS} | R Documentation |
GWCoGAPS
GWCoGAPS(simulationName, nFactor, nCores = NA, cut = NA, minNS = NA, manualMatch = FALSE, consensusPatterns = NULL, saveUnmatchedPatterns = FALSE, ...)
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 |
calls the C++ MCMC code and performs Bayesian matrix factorization returning the two matrices that reconstruct the data matrix for whole genome data;
list of A and P estimates
gapsRun
, patternMatch4Parallel
, and gapsMapRun
data(SimpSim) sim_name <- "example" createGWCoGAPSSets(SimpSim.D, SimpSim.S, nSets=2, sim_name) result <- GWCoGAPS(sim_name, nFactor=3, nEquil=200, nSample=200)