matrix for a pathway objectThis function creates the network matrix representing the gene-gene interaction
structure within a particular pathway. In this process a
KEGG kgml file is downloaded and saved in the working directory.
# S4 method for pathway
get_network_matrix(object, directed = TRUE)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.
A logic argument, stating whether the network matrix
should be returned directed (TRUE) or undirected (FALSE).
The altered pathway object, in which the slots 'adj' and
'sign' have been changed according to the downloaded information on the
pathway.