WAP.int {NetInt}

Weighted Average Per-class (WAP) network integration

Description

It performs the WAP integration between networks: \[\bar{w}_{ij}(k) = \sum_{d = 1}^n \alpha^d(k) w_{ij}^d\] where \[\alpha^d(k) = \frac{1}{\sum_{j=1}^n M^j(k)} M^d(k)\] and \(M^d(k)\) is a suitable accuracy metrics for class k on network d. The metrics could be, e.g. the AUC or the precision at a given recall. Note that this function puts more weight (alpha parameter) for networks with associated larger M.

Usage

WAP.int(m, align = FALSE, logint = FALSE, ...)

Arguments

m

a numeric vector with the values of the metric used to compute the alpha coefficients. It could be e.g. AUC values.

align

logic. If TRUE the numeric matrices passed as arguments are aligned according to the function align.networks (def: FALSE).

logint

logic. If TRUE m is log transformed: -log(1-m), otherwise a linear integration is performed (def: FALSE).

...

a list of numeric matrices. These must be named matrices representing adjacency matrices of the networks. Matrices may have different dimensions, but corresponding elements in different matrices must have the same name.

Value

A list with two elements:

• WAP : the matrix resulting from WAP

• alpha : a numeric vector with the weight coefficients of the networks

Examples

# Create three example networks of different size
set.seed(123);
A1 <- matrix(runif(100, min = 0, max = 1), nrow = 10);
A1[lower.tri(A1)] = t(A1)[lower.tri(A1)];
diag(A1) <- 0;
rownames(A1) <- colnames(A1) <- sample(LETTERS, 10);

A2 <- matrix(runif(49, min = 0, max = 1), nrow = 7);
A2[lower.tri(A2)] = t(A2)[lower.tri(A2)];
diag(A2) <- 0;
rownames(A2) <- colnames(A2) <- rownames(A1)[1:7];

A3 <- matrix(runif(100, min = 0, max = 1), nrow = 10);
A3[lower.tri(A3)] = t(A3)[lower.tri(A3)];
diag(A3) <- 0;
rownames(A3) <- colnames(A3) <- c(rownames(A1)[1:5], c("A", "B", "Z", "K", "Q"));

# Create random vector of accuracy metrics
m <- runif(3, min = 0, max = 1);

# Integrate networks using Weighted Average Per-class (WAP) method
A_int <- WAP.int(m, align=TRUE, logint=FALSE, A1, A2, A3);