cor2adj: Calculate an adjacency matrix from a correlation matrix

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

Calculate an adjacency matrix from a correlation matrix

Description

Calculate an adjacency matrix from a correlation matrix

Usage

cor2adj(cor_matrix, beta, net_type = "signed hybrid")

Arguments

cor_matrix	A numeric, symmetric matrix with pairwise correlations between genes (i.e., a 'correlation matrix').
beta	Numeric scalar indicating the value of the \beta power to which correlation coefficients will be raised to ensure scale-free topology fit.
net_type	Character indicating the type of network to infer. Default: "signed hybrid".

Value

A numeric, symmetric matrix with network adjacency values between genes.

Examples

# Simulate an expression matrix with 100 genes and 50 samples
exp <- matrix(
    rnorm(100 * 50, mean = 10, sd = 2),
    nrow = 100,
    dimnames = list(
        paste0("gene", seq_len(100)),
        paste0("sample", seq_len(50))
    )
)

# Calculate correlation matrix
cor_mat <- exp2cor(exp)

# Calculate adjacency matrix (random value for beta)
adj <- cor2adj(cor_mat, beta = 9)

almeidasilvaf/BioNERO documentation built on March 25, 2024, 9:14 p.m.