get_network_matrix function

Function to calculate the network matrix for a pathway object

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.

## 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'.

Returns

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