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Single Data Set Decomposition with Nonnegative Matrix Factorization

Source: R/sepNMF.R
sepNMF.Rd

Apply NMF (Nonnegative Matrix Factorization) to a single data set

Usage

sepNMF(
  dataset,
  comp_num,
  weighting = NULL,
  perturbation = 1e-04,
  enable_normalization = TRUE,
  column_sum_normalization = FALSE,
  screen_prob = NULL
)

Arguments

dataset

A dataframe/matrix to be decomposed

comp_num

Number of NMFs to be extracted

weighting

Weighting of each dataset, initialized to be NULL

perturbation

A small perturbation to ensure nmf works well

enable_normalization

An argument to decide whether to use normalizaiton or not, default is TRUE

column_sum_normalization

An argument to decide whether to use column sum normalization or not, default it FALSE

screen_prob

A vector of probabilies for genes to be chosen

Value

A list of scores and component

Examples

dataset = list(matrix(runif(5000, 1, 2), nrow = 100, ncol = 50))
comp_num = 2
res_sepNMF = sepNMF(dataset, comp_num)