pwAdjMatrices {PathWave} | R Documentation |
Builds a list of and -if wanted prints- adjacency matrices for a list of bipartite graphs.
pwAdjMatrices(reactionList, compoundList, printMatrices = FALSE, matrixType = "adjacency")
reactionList |
List of reactions. See details. |
compoundList |
List of compounds. See details. |
printMatrices |
Built matrices are printed in the working directory (default FALSE). See details. |
matrixType |
Printed matrices could be of type "adjacency" or "distance" (default "adjacency"). |
A list is returned:
pathway ID |
List of different pathways. |
nNodes |
Integer, number of nodes (reactions) in graph. |
iMax |
Integer, length of longest shortest path between all pairs of reactions in graph. |
M |
Adjacency matrix for the pathway ID. |
dist |
Distance matrix for the pathway ID. |
Gunnar Schramm
See Also as pwKEGGxml
,pwLPFiles
#read in actual KEGG xml files kegg.ftp="ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/" keggXml=pwKEGGxml(kegg.ftp) #build adjacency matrices adjacencyMatrices=pwAdjMatrices(reactionList=keggXml$reactions,compoundList=keggXml$compounds,printMatrices=FALSE)