screen_bic.glasso: BIC-tuned glasso with additional thresholding

In FrankD/nethet: A bioconductor package for high-dimensional exploration of biological network heterogeneity

Description

BIC-tuned glasso with additional thresholding

Usage

screen_bic.glasso(x, include.mean = TRUE, length.lambda = 20,
  lambdamin.ratio = ifelse(ncol(x) > nrow(x), 0.01, 0.001),
  penalize.diagonal = FALSE, plot.it = FALSE,
  trunc.method = "linear.growth", trunc.k = 5, use.package = "huge",
  verbose = FALSE)

Arguments

x	The input data. Needs to be a num.samples by dim.samples matrix.
include.mean	Include mean in likelihood. TRUE / FALSE (default).
length.lambda	Length of lambda path to consider (default=20).
lambdamin.ratio	Ratio lambda.min/lambda.max.
penalize.diagonal	If TRUE apply penalization to diagonal of inverse covariance as well. (default=FALSE)
plot.it	TRUE / FALSE (default)
trunc.method	None / linear.growth (default) / sqrt.growth
trunc.k	truncation constant, number of samples per predictor (default=5)
use.package	'glasso' or 'huge' (default).
verbose	If TRUE, output la.min, la.max and la.opt (default=FALSE).

Value

Returns a list with named elements 'rho.opt', 'wi', 'wi.orig', Variable rho.opt is the optimal (scaled) penalization parameter (rho.opt=2*la.opt/n). The variables wi and wi.orig are matrices of size dim.samples by dim.samples containing the truncated and untruncated inverse covariance matrix.

Author(s)

n.stadler

Examples

n=50
p=5
x=matrix(rnorm(n*p),n,p)
wihat=screen_bic.glasso(x,length.lambda=5)$wi

FrankD/nethet documentation built on Oct. 5, 2020, 8:22 a.m.