lassoSEM | R Documentation |
Upon lambda_max to lambda_min in 20 step, the function compute 5 fold CV to determine the optimal lambda for the data.
lassoSEM(Y, X, Missing, B, verbose = 5)
Y |
gene expression M by N matrix |
X |
The network node attribute matrix with dimension of M by N. Theoretically, X can be L by N matrix, with L being the total
node attributes. In current implementation, each node only allows one and only one attribute. |
Missing |
missing data in Y |
B |
true network topology if available |
verbose |
describe the information output from -1 - 10, larger number means more output |
the function perform CV and parameter inference, calculate power and FDR
Bout |
the matrix B from SEM |
fout |
f: the weight for matrix X |
stat |
compute the power and FDR statistics if the ture topology is provided |
simTime |
computational time |
Anhui Huang
1. Cai, X., Bazerque, J.A., and Giannakis, G.B. (2013). Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations. PLoS Comput Biol 9, e1003068.
2. Huang, A. (2014). "Sparse model learning for inferring genotype and phenotype associations." Ph.D Dissertation. University of Miami(1186).
library(sparseSEM)
data(B);
data(Y);
data(X);
data(Missing);
## Not run: OUT <- lassoSEM(Y, X, Missing, B, verbose = 0);
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