rags2ridges: Union – R documentation

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Union

Subset 2 square matrices to union of variables having nonzero entries

Description

Convenience function that subsets 2 square matrices (over the same features) to the union of features that have nonzero row (column) entries (i.e., features implied in graphical connections).

Usage

Union(M1, M2)

Arguments

`M1`	(Possibly sparsified) square `matrix`.
`M2`	(Possibly sparsified) square `matrix` over the same features as `M1`.

Details

Say you have 2 class-specific precision matrices that are estimated over the same variables/features. For various reasons (such as, e.g., the desire to visualize pruned class-specific networks in the same coordinates) one may want to prune these matrices to those features that are implied in graphical connections in at least 1 class.

Value

An object of class list:

`M1subset`	A pruned `matrix` for class 1.
`M2subset`	A pruned `matrix` for class 2.

Author(s)

Carel F.W. Peeters <cf.peeters@vumc.nl>

Examples

## Invoke data
data(ADdata)

## Subset
ADclass1 <- ADmetabolites[, sampleInfo$ApoEClass == "Class 1"]
ADclass2 <- ADmetabolites[, sampleInfo$ApoEClass == "Class 2"]

## Transpose data
ADclass1 <- t(ADclass1)
ADclass2 <- t(ADclass2)

## Correlations for subsets
rAD1 <- cor(ADclass1)
rAD2 <- cor(ADclass2)

## Simple precision estimates
P1 <- ridgeP(rAD1, 2)
P2 <- ridgeP(rAD2, 2)
Plist = list(P1 = P1, P2 = P2)

## Threshold matrices
Mats <- sparsify.fused(Plist, threshold = "top", top = 20)

## Prune sparsified partial correlation matrices
## To union of features implied by edge
MatsPrune <- Union(Mats$P1$sparseParCor, Mats$P2$sparseParCor)

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