parseKGML2DataFrame {KEGGgraph} | R Documentation

## 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`

### 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.

### Value

A three-column data frame, representing the graph structure: out-nodes (the `from` column), in-nodes (`to`) and edge subtype (`subtype`).

### Author(s)

Jitao David Zhang

### 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

[Package KEGGgraph version 1.40.0 Index]