JGL: Performs the Joint Graphical Lasso for sparse inverse covariance estimation on multiple classes

The Joint Graphical Lasso is a generalized method for estimating Gaussian graphical models/ sparse inverse covariance matrices/ biological networks on multiple classes of data. We solve JGL under two penalty functions: The Fused Graphical Lasso (FGL), which employs a fused penalty to encourage inverse covariance matrices to be similar across classes, and the Group Graphical Lasso (GGL), which encourages similar network structure between classes. FGL is recommended over GGL for most applications.

Author
Patrick Danaher
Date of publication
2013-04-16 21:27:09
Maintainer
Patrick Danaher <pdanaher@uw.edu>
License
GPL-2
Version
2.3

View on CRAN

Man pages

crit
Calculate the critical value of the FGL objective funciton.
example.data
Toy two-class gene expression dataset.
gcrit
Calculate the critical value of the GGL objective funciton.
JGL
Joint Graphical Lasso
JGL-internal
Internal JGL functions
JGL-package
Joint Graphical Lasso
net.degree
List the degree of every node in all classes.
net.edges
List the edges in a network
net.hubs
Get degrees of most connected nodes.
net.neighbors
Get network neighbors of a node
screen.fgl
Quickly identify connected features in the solution to FGL
screen.ggl
Quickly identify connected features in the solution to GGL
subnetworks
Identify subnetwork membership

Files in this package

JGL
JGL/MD5
JGL/data
JGL/data/example.data.rda
JGL/man
JGL/man/crit.Rd
JGL/man/screen.ggl.Rd
JGL/man/JGL-internal.Rd
JGL/man/net.degree.Rd
JGL/man/gcrit.Rd
JGL/man/example.data.Rd
JGL/man/JGL.Rd
JGL/man/net.hubs.Rd
JGL/man/screen.fgl.Rd
JGL/man/subnetworks.Rd
JGL/man/net.neighbors.Rd
JGL/man/JGL-package.Rd
JGL/man/net.edges.Rd
JGL/R
JGL/R/admm.iters.r
JGL/R/net.edges.R
JGL/R/screen.fgl.R
JGL/R/make.adj.matrix.R
JGL/R/penalty.as.matrix.R
JGL/R/gcrit.R
JGL/R/admm.iters.unconnected.r
JGL/R/subnetworks.R
JGL/R/flsa2.R
JGL/R/crit.R
JGL/R/screen.ggl.R
JGL/R/soft.R
JGL/R/net.degree.R
JGL/R/flsa.general.R
JGL/R/JGL.r
JGL/R/net.neighbors.R
JGL/R/net.hubs.R
JGL/R/dsgl.R
JGL/DESCRIPTION
JGL/NAMESPACE