rags2ridges: adjacentMat – R documentation

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adjacentMat

Transform real matrix into an adjacency matrix

Description

Function that transforms a real matrix into an adjacency matrix. Intended use: Turn sparsified precision matrix into an adjacency matrix for undirected graphical representation.

Usage

adjacentMat(M, diag = FALSE)

Arguments

`M`	(Possibly sparsified precision) `matrix`.
`diag`	A `logical` indicating if the diagonal elements should be retained.

Value

Function returns an adjacency matrix.

Author(s)

Carel F.W. Peeters <cf.peeters@vumc.nl>, Wessel N. van Wieringen

Examples

## Obtain some (high-dimensional) data
p = 25
n = 10
set.seed(333)
X = matrix(rnorm(n*p), nrow = n, ncol = p)
colnames(X)[1:25] = letters[1:25]
Cx <- covML(X)

## Obtain regularized precision matrix
P <- ridgeP(Cx, lambda = 10, type = "Alt")

## Obtain sparsified partial correlation matrix
PC0 <- sparsify(P, threshold = "localFDR", FDRcut = .8)

## Obtain adjacency matrix
adjacentMat(PC0$sparsePrecision)

rags2ridges

Ridge Estimation of Precision Matrices from High-Dimensional Data

v2.2.4

GPL (>= 2)

Authors

Carel F.W. Peeters [cre, aut], Anders Ellern Bilgrau [aut], Wessel N. van Wieringen [aut]

Initial release