AdjacencyMatrix-class: Methods for 'AdjacencyMatrix' objects

In tnaake/MetNet: Inferring metabolic networks from untargeted high-resolution mass spectrometry data

Methods for 'AdjacencyMatrix' objects

Description

'length' returns the length of an 'AdjacencyMatrix' object (number of rows of an assay). 'length' returns a 'numeric' of length 1.

'dim' returns the length of an 'AdjacencyMatrix' object (number of rows of an assay, number of cols of an assay). 'dim' returns a 'numeric' of length 2.

'type' will return the type of an 'AdjacencyMatrix' ('statistical', 'structural' or 'combine'). 'type' returns a 'character' of length 1

'directed' returns the information on directed of an 'AdjacencyMatrix', i.e. if the underlying graph is directed or undirected. 'directed' returns 'logical' of length 1.

'thresholded' returns the information if the adjacency matrix is thresholded, i.e. if the function 'rtCorrection' or 'threshold' was applied to the 'AdjacencyMatrix' object. 'thresholded' returns a 'logical' of length 1.

'show' prints summary information on an object of class 'AdjacencyMatrix'.

'as.data.frame' returns the adjacency matrices (stored in the 'assays' slot) and returns information on the nodes and the associated information on edges as a data frame. 'as.data.frame' returns a 'data.frame'.

Usage

## S4 method for signature 'AdjacencyMatrix'
length(x)

## S4 method for signature 'AdjacencyMatrix'
dim(x)

## S4 method for signature 'AdjacencyMatrix'
type(x)

## S4 method for signature 'AdjacencyMatrix'
directed(object)

## S4 method for signature 'AdjacencyMatrix'
thresholded(object)

## S4 method for signature 'AdjacencyMatrix'
show(object)

## S4 method for signature 'AdjacencyMatrix'
as.data.frame(x)

Arguments

x	instance of class 'AdjacencyMatrix'
object	instance of class 'AdjacencyMatrix'

Author(s)

Thomas Naake, [e-mail]

tnaake/MetNet documentation built on Nov. 4, 2024, 4:45 a.m.