Description Usage Arguments Value Examples
'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.
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)
|
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 |
'NMF_RNA_Tang' returns the resulted W and H, as well as track of errors along iteration
1 2 |
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