Description Usage Arguments Value
Implementing FSSELM algorithm for network inference. If Xs is identify for different conditions, multiFSSEMiPALM will be use, otherwise, please
use multiFSSEMiPALM2
for general cases
1 2 3 4 |
Xs |
eQTL matrices |
Ys |
Gene expression matrices |
Bs |
initialized GRN-matrices |
Fs |
initialized eQTL effect matrices |
Sk |
eQTL index of genes |
sigma2 |
initialized noise variance from ridge regression |
lambda |
Hyperparameter of lasso term in FSSEM |
rho |
Hyperparameter of fused-lasso term in FSSEM |
Wl |
weight matrices for adaptive lasso terms |
Wf |
weight matrix for adaptive fused lasso term |
p |
number of genes |
maxit |
maximum iteration number. Default 100 |
inert |
inertial function for iPALM. Default as k-1/k+2 |
threshold |
convergence threshold. Default 1e-6 |
verbose |
Default TRUE |
sparse |
Sparse Matrix or not |
trans |
Fs matrix is transposed to k x p or not. If Fs from ridge regression, trans = TRUE, else, trans = FALSE |
B2norm |
B2norm matrices generated from ridge regression. Default NULL. |
strict |
Converge strictly or not. Default False |
fit List of FSSEM model
coefficient matrices of gene regulatory networks
coefficient matrices of eQTL-gene effect
Bias vector
estimate of covariance in SEM
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