createStatisticalAdjacencyList {MetNet}R Documentation

Create a list of statistical adjacency matrices

Description

The function infers adjacency matrix topologies from statistical methods and returns matrices of these networks in a list. The function includes functionality to caluclate adjacency matrices based on LASSO (L1 norm)-regression, random forests, context likelihood of relatedness (CLR), the algorithm for the reconstruction of accurate cellular networks (ARACNE), Pearson correlation (also partial and semipartial), Spearman correlation (also partial and semipartial) and Constraint-based structure learning (Bayes). The function returns a list of adjacency matrices that are defined by model.

Usage

createStatisticalAdjacencyList(x, model, ...)

Arguments

x

matrix that contains intensity values of features/metabolites (rows) per sample (columns).

model,

character vector containing the methods that will be used ("lasso", "randomForest", "clr", "aracne", "pearson", "pearson_partial", "pearson_semipartial","spearman", "spearman_partial", "spearman_semipartial", "bayes")

...

parameters passed to the functions lasso, randomForest, clr, aracne, correlation and/or bayes

Details

createStatisticalAdjacencyList calls the function lasso, randomForest, clr, aracne, correlation (for "pearson", "pearson_partial", "pearson_semipartial", "spearman", "spearman_partial", "spearman_semipartial") and/or bayes as specified by model. It will create adjacency matrices using the specified methods and will return a list containing the unweighted adjacency matrix (if model is of length 1) or append these unweighted adjacency matrices to a list (if model is of length > 1). Internally x will be z-scaled and the z-scaled object will be used in lasso, clr and/or aracne.

Value

list containing the respective adjacency matrices specified by model

Author(s)

Thomas Naake, thomasnaake@googlemail.com

Examples

data("x_test", package="MetNet")
x <- x_test[, 3:dim(x_test)[2]]
x <- as.matrix(x)
createStatisticalAdjacencyList(x, c("pearson", "spearman"))

[Package MetNet version 1.2.0 Index]