concatNMF: Concatenated decomposition with Nonnegative Matrix...

In CHuanSite/SJD: Structured Joint Decomposition (SJD)

Concatenated decomposition with Nonnegative Matrix Factorization

Description

Concatenated decomposition of several matrices with Nonnegative Matrix Factorization (NMF)

Usage

concatNMF(
  dataset,
  group,
  comp_num,
  weighting = NULL,
  perturbation = 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
perturbation	the perturbation of the 0 element in the analysis
proj_dataset	The dataset(s) to be projected on.
proj_group	A listed of boolean combinations indicating which groupings should be used for each projected dataset.The length of proj_group should match the length of proj_dataset, and the length of each concatenated boolean combination should match the length of the parameter group.
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 concatNMF 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 = list(matrix(runif(5000, 1, 2), nrow = 100, ncol = 50))
proj_group = list(c(TRUE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE))
res_concatNMF = concatNMF(
dataset,
group,
comp_num,
proj_dataset = proj_dataset,
proj_group = proj_group)

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