opt.multiFSSEMiPALM2: opt.multiFSSEMiPALM2

In fssemR: Fused Sparse Structural Equation Models to Jointly Infer Gene Regulatory Network

opt.multiFSSEMiPALM2

Description

optimize multiFSSEMiPALM's parameters by minimize BIC, when feature size is large (> 300), BIC methods will be much faster than Cross-validation

Usage

opt.multiFSSEMiPALM2(
  Xs,
  Ys,
  Bs,
  Fs,
  Sk,
  sigma2,
  nlambda = 20,
  nrho = 20,
  p,
  q,
  wt = TRUE
)

Arguments

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
nlambda	number of hyper-parameter of lasso term in CV
nrho	number of hyper-parameter of fused-lasso term in CV
p	number of genes
q	number of eQTLs
wt	use adaptive lasso or not. Default TRUE.

Value

list of model selection result

Examples

seed = 1234
N = 100                                           # sample size
Ng = 5                                            # gene number
Nk = 5 * 3                                        # eQTL number
Ns = 1                                            # sparse ratio
sigma2 = 0.01                                     # sigma2
set.seed(seed)
library(fssemR)
data = randomFSSEMdata(n = N, p = Ng, k = Nk, sparse = Ns, df = 0.3, sigma2 = sigma2,
                       u = 5, type = "DG", nhub = 1, dag = TRUE)
## If we assume that different condition has different genetics perturbations (eQTLs)
data$Data$X = list(data$Data$X, data$Data$X)
## gamma = cv.multiRegression(data$Data$X, data$Data$Y, data$Data$Sk, ngamma = 20, nfold = 5,
##                            N, Ng, Nk)
gamma = 0.6784248     ## optimal gamma computed by cv.multiRegression
fit   = multiRegression(data$Data$X, data$Data$Y, data$Data$Sk, gamma, N, Ng, Nk,
                      trans = FALSE)
Xs    = data$Data$X
Ys    = data$Data$Y
Sk    = data$Data$Sk

fitm <- opt.multiFSSEMiPALM2(Xs = Xs, Ys = Ys, Bs = fit$Bs, Fs = fit$Fs, Sk = Sk,
                           sigma2 = fit$sigma2, nlambda = 10, nrho = 10,
                           p = Ng, q = Nk, wt = TRUE)

fitc0 <- fitm$fit

(TPR(fitc0$Bs[[1]], data$Vars$B[[1]]) + TPR(fitc0$Bs[[2]], data$Vars$B[[2]])) / 2
(FDR(fitc0$Bs[[1]], data$Vars$B[[1]]) + FDR(fitc0$Bs[[2]], data$Vars$B[[2]])) / 2
TPR(fitc0$Bs[[1]] - fitc0$Bs[[2]], data$Vars$B[[1]] - data$Vars$B[[2]])
FDR(fitc0$Bs[[1]] - fitc0$Bs[[2]], data$Vars$B[[1]] - data$Vars$B[[2]])

fssemR documentation built on March 18, 2022, 7:24 p.m.