| parseKGML2DataFrame {KEGGgraph} | R Documentation |
This function extends the parseKGML2Graph function, by
converting the resulting graph into a three-column data frame
representing out-nodes (the from column in the data frame),
in-nodes (to) and subtypes of edges that connect
them (subtype). It can be used, for example, for exporting KEGG pathway networks
in plain text files.
parseKGML2DataFrame(file, reactions=FALSE,...)
file |
A KGML file |
reactions |
Logical, whether metabolic reactions should be parsed
and returned as part of the data frame. Default: |
... |
Other parameters passed to |
The out- and in-nodes are represented in the form of KEGG
identifiers. For human EntrezIDs the function
translateKEGGID2GeneID can be used.
Multile edges are supported: in case more than one subtypes of edges exist between two nodes, they are all listed in the resulting data frame.
A three-column data frame, representing the graph structure:
out-nodes (the from column), in-nodes (to) and edge
subtype (subtype).
Jitao David Zhang
parseKGML2Graph, KEGGpathway2Graph and translateKEGGID2GeneID.
sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
gdf <- parseKGML2DataFrame(sfile)
head(gdf)
dim(gdf)
rfile <- system.file("extdata/hsa00020.xml",package="KEGGgraph")
dim(dfWr <- parseKGML2DataFrame(rfile, reactions=TRUE))
dim(dfWOr <- parseKGML2DataFrame(rfile, reactions=FALSE))
stopifnot(nrow(dfWr)>nrow(dfWOr))
## not expanding genes: only the KGML-specific identifiers are used then
## only for expert use
## NOT RUN
gdf.ne <- parseKGML2DataFrame(sfile, expandGenes=FALSE)
dim(gdf.ne)
head(gdf.ne)
## NOT RUN