Union {rags2ridges} | R Documentation |
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 |
M2 |
(Possibly sparsified) square |
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 |
M2subset |
A pruned |
Author(s)
Carel F.W. Peeters <carel.peeters@wur.nl>
See Also
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)