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]