NMF_RNA_Tang: NMF core function

In tdw1221/NITUMID: Non-negative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution

Description

‘NMF_RNA_Tang' is the core function for NITUMID’s factorization, it takes the gene expression matrix Y, guide matrix A, initial W and H, as well as other parameters as input, and optimizes til converged/ or reached maximum steps

Usage

NMF_RNA_Tang(Y, ini.W, ini.H, lam_W, beta_W, A, eta, tol = 10^-5,
  prterr = F, max.itr = 2000, always = T)

Arguments

Y	Y is the gene expression matrix that has #signature genes rows and #samples columns
ini.W	Initial W matrix
ini.H	Initial H matrx
lam_W	$\lambda$ is the parameter imposing A's structure into resulting W, see our paper for more info. In real calculation, upper level functions will automatically choose suitable $\lambda$ no need to set by yourself
beta_W	$\beta$ is the parameter controlling sparsity ridge penalty, see our paper for more information. In real calculation, upper level functions will automatically choose suitable $\beta$ no need to set by yourself
A	The trichotomous guide matrix A
eta	$\eta$ is the parameter for ensuring column sums of H are 1s, upper level function will choose suitable $\eta$ automatically, no need to spcify yourself
tol	numeric scalar, the cutoff value for stop iterating, default $10^-5$
prterr	logical value indicating if it should print each step's error, default FALSE
max.itr	numerical scalar, maximum iteration number, default 2000
alaways	logical, if it should output results whatsover when max.itr is reached, default TRUE

Value

'NMF_RNA_Tang' returns the resulted W and H, as well as track of errors along iteration

tdw1221/NITUMID documentation built on May 31, 2019, 1:54 a.m.