gapsMapRun {CoGAPS}R Documentation

Backwards Compatibility with v2

Description

Backwards Compatibility with v2

Usage

gapsMapRun(D, S, FP, ABins = data.frame(), PBins = data.frame(),
  nFactor = 5, simulation_id = "simulation", nEquil = 1000,
  nSample = 1000, nOutR = 1000, output_atomic = FALSE,
  fixedMatrix = "P", 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

FP

data.frame with rows giving fixed patterns for P

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

fixedMatrix

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

...

v2 style parameters

Value

list with A and P matrix estimates

Examples

data(SimpSim)
nC <- ncol(SimpSim.D)
patterns <- matrix(1:nC/nC, nrow=1, ncol=nC)
result <- gapsMapRun(SimpSim.D, SimpSim.S, FP=patterns, nFactor=3)

[Package CoGAPS version 3.0.2 Index]