GWCoGAPS: GWCoGAPS

In genesofeve/GWCoGAPS:

Description

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

Usage

GWCoGAPS(nCores = NA, D, S, nFactor, nSets, Cut = NA,
  saveBySetResults = FALSE, fname = fname,
  PatternsMatchFN = postCoGAPSPatternMatch, manualMatch = FALSE,
  numSnapshots = numSnapshots, minNS = NA, ...)

Arguments

D	data matrix
S	uncertainty matrix (std devs for chi-squared of Log Likelihood)
nFactor	number of patterns (basis vectors, metagenes), which must be greater than or equal to the number of rows of FP
nSets	number of sets for parallelization
numSnapshots	the number of individual samples to capture
FP	data.frame with rows giving fixed patterns for P
ABins	a matrix of same size as A which gives relative probability of that element being non-zero
PBins	a matrix of same size as P which gives relative probability of that element being non-zero
simulation_id	name to attach to atoms files if created
nEquil	number of iterations for burn-in
nSample	number of iterations for sampling
nOutR	how often to print status into R by iterations
output_atomic	whether to write atom files (large)
sampleSnapshots	Boolean to indicate whether to capture individual samples from Markov chain during sampling
alphaA	sparsity parameter for A domain
max_gibbmass_paraA	limit truncated normal to max size
alphaP	sparsity parameter for P domain
max_gibbmass_paraP	limit truncated normal to max size

Value

list with A and P matrix estimates, chi-squared and atom numbers of sample by iteration, and chi-squared of mean

See Also

CoGAPS

Examples

## Not run: 
GWCoGAPS(nCores=NA, D, S, nFactor, nSets,saveBySetResults=TRUE, fname=fname,
PatternsMatchFN = patternMatch4Parallel,numSnapshots=numSnapshots,minNS=minNS)

## End(Not run)

genesofeve/GWCoGAPS documentation built on May 17, 2019, 1:10 a.m.