KEGGgraph (version 1.30.0)

parseKGML2DataFrame: Parse KGML file into a data frame

Description

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.

Usage

parseKGML2DataFrame(file, reactions=FALSE,...)

Arguments

file

A KGML file

reactions

Logical, whether metabolic reactions should be parsed and returned as part of the data frame. Default:FALSE

...

Other parameters passed to KEGGpathway2Graph

Value

out-nodes (the from column), in-nodes (to) and edge subtype (subtype).

Details

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.

See Also

parseKGML2Graph, KEGGpathway2Graph and translateKEGGID2GeneID.

Examples

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