run_scINSIGHT | R Documentation |
Perform INterpreting single cell gene expresSIon bioloGically Heterogeneous daTa (scINSIGHT) to return factorized W_{\ell1}, W_{\ell2}, H and V matrices.
This factorization produces a W_{\ell1} matrix (cells by K_j), a W_{\ell2} matrix (cells by K), a shared V matrix (K by genes) for each sample, and a H (K_j by genes) matrix for each condition. W_{\ell2} are the expression matrices of K common gene modules for all samples, V is the membership matrix of K common gene modules, and it's shared by all samples. W_{\ell1} are the expression matrices of K_j condition-specific gene modules for all samples, and H are the membership matrices of K_j condition-specific gene modules for all conditions.
run_scINSIGHT( object, K = seq(5, 15, 2), K_j = 2, LDA = c(0.001, 0.01, 0.1, 1, 10), thre.niter = 500, thre.delta = 0.01, num.cores = 1, B = 5, out.dir = NULL, method = "increase" )
object |
|
K |
Number of common gene modules. (default |
K_j |
Number of dataset-specific gene modules. (default 2) |
LDA |
Regularization parameters. (default |
thre.niter |
Maximum number of block coordinate descent iterations to perform. (default 500) |
thre.delta |
Stop iteration when the reduction of objective function is less than the threshold. (default 0.01) |
num.cores |
Number of cores used for optimizing factorizations in parallel (default 1). |
B |
Number of repeats with random seed from 1 to B. (default 5) |
out.dir |
Output directory of scINSIGHT results. (default NULL) |
method |
Method of updating the factorization (default "increase"). If provide multiple K, user can choose method between "increase" and "decrease". For "increase", the algorithm will first perform factorization with the least K=K_1. Then initialize K_2-K_1 facotrs, where K_2 is the K sightly larger than K_1, and perform facotrization with these new facotrs. Continue this process until the largest K. For "increase", the algorithm will first perform factorization with the largest K=K_1. Then choose K_2 facotrs, where K_2 is the K sightly less than K_1, and perform facotrization with these new facotrs. Continue this process until the least K. |
scINSIGHT
object with W_1, W_2, H, V and parameters slots set.
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