FitSparsePCA: Fit sparse PCA on a grid of alpha

In Rmomal/VEMtree: Network inference from Species counTs with missing actORs

Description

Fit sparse PCA on a grid of alpha

Usage

FitSparsePCA(M, r = 1, min.size = 1, alphaGrid = 10^(seq(-4, 0, by = 0.1)))

Arguments

M	Gaussian proxy for the original dataset. Possibly obtained using PLNmodels.
r	Number of missing actors.
min.size	Minimal number of neighbors for each missing actor.
alphaGrid	Grid for parsity controlling parameter.

Value

• sPcaOpt: optimal spca object.

• alphaOpt: best alpha value among the provided grid.

• loglik: vector of log likelihood obtained for each value of alpha.

• bic: vecotr of BIC values.

• cliques: optimal clique of neighbors.

Examples

data=generate_missing_data(n=100,p=10,r=1,type="scale-free", plot=TRUE)
TrueClique=data$TC
PLNfit=norm_PLN(data$Y)
findclique=FitSparsePCA(PLNfit$MO,r=1)
initClique=findclique$cliques
TrueClique
initClique

Rmomal/VEMtree documentation built on Dec. 17, 2020, 5:17 p.m.