gapsRun {CoGAPS}R Documentation

Backwards Compatibility with v2

Description

Backwards Compatibility with v2

Usage

gapsRun(D, S, ABins = data.frame(), PBins = data.frame(), nFactor = 7,
  simulation_id = "simulation", nEquil = 1000, nSample = 1000,
  nOutR = 1000, output_atomic = FALSE, fixedBinProbs = FALSE,
  fixedDomain = "N", sampleSnapshots = TRUE, numSnapshots = 100,
  alphaA = 0.01, nMaxA = 1e+05, max_gibbmass_paraA = 100, alphaP = 0.01,
  nMaxP = 1e+05, max_gibbmass_paraP = 100, seed = -1, messages = TRUE)

Arguments

D

data matrix

S

uncertainty matrix

ABins

unused

PBins

unused

nFactor

number of patterns (basis vectors, metagenes), which must be greater than or equal to the number of rows of FP

simulation_id

unused

nEquil

number of iterations for burn-in

nSample

number of iterations for sampling

nOutR

number of output messages

output_atomic

unused

fixedBinProbs

unused

fixedDomain

unused

sampleSnapshots

indicates if snapshots should be made

numSnapshots

how many snapshots to take

alphaA

sparsity parameter for A domain

nMaxA

unused

max_gibbmass_paraA

limit truncated normal to max size

alphaP

sparsity parameter for P domain

nMaxP

unused

max_gibbmass_paraP

limit truncated normal to max size

seed

a positive seed is used as-is, while any negative seed tells the algorithm to pick a seed based on the current time

messages

display progress messages

Value

list with A and P matrix estimates

Examples

data(SimpSim)
result <- gapsRun(SimpSim.D, SimpSim.S, nFactor=3)

[Package CoGAPS version 3.0.2 Index]