kangar00: get_network_matrix – R documentation

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get_network_matrix

Function to calculate the network matrix for a pathway object

Description

get_network_matrix creates the adjacency matrix representing the gene-gene interaction structure within a particular pathway. Note that a KEGG kgml file is downloaded and saved in the working directory.

Usage

## S4 method for signature 'pathway'
get_network_matrix(object, directed = TRUE,
  method = "auto")

Arguments

`object`	A `pathway` object identifying the pathway for which gene interaction infomation should be extracted. Here, KEGG IDs of format 'hsa00100' are used and information is downloaded from the KEGG database.
`directed`	A `logical` argument, stating whether the network matrix should return directed (`TRUE`) or undirected (`FALSE`) links.
`method`	Download method to be used for downloading files, passed to via `KEGGgraph::retrieveKGML` to `utils::download.file` function. Currently supports `'auto'` (default), `'internal'`, `'wininet'` (Windows only), `'libcurl'`, `'wget'` and `'curl'`.

Value

get_network_matrix returns the modified pathway object, where the slots adj and sign are altered according to the downloaded information in the KEGG kgml file.

Author(s)

Stefanie Friedrichs, Patricia Burger, Juliane Manitz

kangar00

Kernel Approaches for Nonlinear Genetic Association Regression

v1.4

GPL-2

Authors

Juliane Manitz [aut], Stefanie Friedrichs [aut], Patricia Burger [aut], Benjamin Hofner [aut], Ngoc Thuy Ha [aut], Saskia Freytag [ctb], Heike Bickeboeller [ctb]

Initial release

2020-02-12