runNMF {spectralAnalysis}

Actual NMF analysis

Description

Actual NMF analysis

Usage

runNMF(
  spectra,
  rank,
  method = "PGNMF",
  seed = NULL,
  nruns = 10,
  checkDivergence = TRUE,
  timePointsList = NULL,
  subsamplingFactor = 3,
  maxIter = 1000
)

Arguments

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 TRUE

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

Value

Resulting NMF model (in accordance with the NMF package definition)

Author(s)

Nicolas Sauwen