Usage
KEGG2Pathway(file, expandGenes = TRUE, expandCom = TRUE, nongene = c("keep", "propagate", "discard"), ident = "KEGGnative", database = "KEGG", species = NULL)
Arguments
file
Character, the name of the file to be parsed. Download manually or in bulk from KEGG
expandGenes
Logical, should multi-gene nodes be expanded into separate nodes?
expandCom
Logical, should undirected binding interactions be added between nodes from one group (usually multi-subunit protein complex, which is turned into a clique)
nongene
Character, how should be the non-gene nodes parsed? If "discard" they are removed from the pathway. If "propagate", they are removed but the interactions are preserved (e.g. if gene A interacts with compound c and compound c interacts with gene B, then the interaction between A and B is preserved. Otherwise, they are kept in the pathway topology
ident
Character, the type of the node identifiers.
database
Character, the name of the database
species
Character, the three-letter code for the species-specific pathways. If NULL then, the first 3 letters from the file are used.