# NMF_RNA_Tang_ind: NMF core function In tdw1221/NITUMID: Non-negative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution

## Description

'NMF_RNA_Tang_ind' is a upper level wrapper function for 'NMF_RNA_Tang'. On top of core NMF, it also initialtes $W$ and $H$, and scales/normalizes according to the input arguments: scale_Data and reg_para. Besides, it also does random permutations to check results stability and helps choose the best parameters. Although it has full sets of NITUMID's functions, the 'NMF_RNA_Tang_ind' is still not supposed to be run independently, has hyper-function will call it with different parameters choices.

## Usage

 1 2 3 NMF_RNA_Tang_ind(Y, lam_W, beta_W, A, eta, tol = 10^-5, prterr = F, max.itr = 2000, always = F, num_cell = 11, scale_Data, perm_type = T) 

## Arguments

 Y Y is the gene expression matrix that has #signature genes rows and #samples columns 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 num_cell numeric scalar, number of component cell types, dfault 11. Noted that if you were to change component cell types number, you should change your $A$ matrix accordingly. scale_Data the parameter controlling which scaling method to use for $Y$: 0 indicates no scaling, 1 indicates scaling $||Y||_F=\sqrtnm$, where $n,m$ are dimensions of Y; 2 indicates scaling such that $||Y^scaled||_F=||log(Y^raw+1)||_F$ perm_type logical variable, default TRUE. If TRUE, the function will do a permutation and measure consistency between results. ini.W Initial W matrix ini.H Initial H matrx 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

## Examples

 1 2 This function is not supposed to be run independently, it is supposed to be called by top level function, which will feed it with different pre-determined parameters and choose thr best one 

tdw1221/NITUMID documentation built on Jan. 17, 2019, 12:46 a.m.