runNMF | R Documentation |
Actual NMF analysis
runNMF( spectra, rank, method = "PGNMF", seed = NULL, nruns = 10, checkDivergence = TRUE, timePointsList = NULL, subsamplingFactor = 3, maxIter = 1000 )
spectra |
spectral input matrix, with wavelengths as its rows and time points as its columns |
rank |
number of NMF components to be found |
method |
name of the NMF method to be used, consult the help of the 'nmf' function from the NMF package for the methods available by default |
seed |
nmfModel object containing initialization of the factor matrices |
nruns |
number of NMF runs. It is recommended to run the NMF analyses multiple times when random seeding is used, to avoid a suboptimal solution |
checkDivergence |
Boolean indicating whether divergence checking should be performed, defaults to |
timePointsList |
list of time point vectors of the individual experiments |
subsamplingFactor |
subsampling factor used during NMF analysis |
maxIter |
maximum number of iterations per NMF run |
Resulting NMF model (in accordance with the NMF package definition)
Nicolas Sauwen
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