jointNMF: Joint Decomposition with Nonnegative Matrix Factorization

In CHuanSite/SJD: Structured Joint Decomposition (SJD)

Joint Decomposition with Nonnegative Matrix Factorization

Description

Joint decomposition of several linked matrices with Nonnegative Matrix Factorization (NMF) It is based on the MSE loss, proposed by Lee, Daniel D., and H. Sebastian Seung. "Learning the parts of objects by non-negative matrix factorization." Nature 401.6755 (1999): 788-791.

Usage

jointNMF(
  dataset,
  group,
  comp_num,
  weighting = NULL,
  max_ite = 1000,
  max_err = 1e-04,
  proj_dataset = NULL,
  proj_group = NULL,
  enable_normalization = TRUE,
  column_sum_normalization = FALSE,
  screen_prob = NULL
)

Arguments

dataset	A list of dataset to be analyzed
group	A list of grouping of the datasets, indicating the relationship between datasets
comp_num	A vector indicates the dimension of each compoent
weighting	Weighting of each dataset, initialized to be NULL
max_ite	The maximum number of iterations for the jointNMF algorithms to run, default value is set to 100
max_err	The maximum error of loss between two iterations, or the program will terminate and return, default value is set to be 0.0001
proj_dataset	The dataset to be projected on.
proj_group	A boolean combination indicating which groupings should be used for the projected dataset.
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 contains the component and the score of each dataset on every component after jointNMF algorithm

Examples

dataset = list(matrix(runif(5000, 1, 2), nrow = 100, ncol = 50),
matrix(runif(5000, 1, 2), nrow = 100, ncol = 50),
matrix(runif(5000, 1, 2), nrow = 100, ncol = 50),
matrix(runif(5000, 1, 2), nrow = 100, ncol = 50))
group = list(c(1,2,3,4), c(1,2), c(3,4), c(1,3), c(2,4), c(1), c(2), c(3), c(4))
comp_num = c(2,2,2,2,2,2,2,2,2)
proj_dataset = matrix(runif(5000, 1, 2), nrow = 100, ncol = 50)
proj_group = c(TRUE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE)
res_jointNMF = jointNMF(
dataset,
group,
comp_num,
proj_dataset = proj_dataset,
proj_group = proj_group)

CHuanSite/SJD documentation built on Nov. 29, 2024, 5:52 a.m.