Update all KEGG pathway networks and calculate their NS scores

Update all KEGG pathway networks and calculate their NS scores

update_all_pathway_NS(pathway_xml_ls = NULL, org = NULL, lambda = 0.5)

Arguments

pathway_xml_ls

A list of KEGG pathway XML files, where each element is a `tbl_graph` or `igraph` object. If `NULL`, it will load the existing XML files.

org

Character, the KEGG organism code (e.g., "hsa" for human). If `NULL`, uses "ko" as the default prefix for pathway IDs.

lambda

Numeric, a parameter for weighting the normalized degree and downstream node count. Default is `0.5`.

See also

calculate_NS