parseKGML2DataFrame: Parse KGML file into a data frame

In KEGGgraph: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

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), types and subtypes of edges that connect them (type and subtype, respectively). 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 four-column data frame, representing the graph structure: out-nodes (the from column), in-nodes (to), edge type (type) and 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

Example output

Attaching package: 'KEGGgraph'

The following object is masked from 'package:graphics':

    plot

      from        to    subtype
1 hsa:5923 hsa:22800 activation
2 hsa:5923 hsa:22808 activation
3 hsa:5923  hsa:3265 activation
4 hsa:5923  hsa:3845 activation
5 hsa:5923  hsa:4893 activation
6 hsa:5923  hsa:6237 activation
[1] 1029    3
[1] 130   3
[1] 101   3
[1] 184   3
  from to           subtype
1    2 32        activation
2    3 18        inhibition
3    3 18 dephosphorylation
4    4 18        inhibition
5    4 18 dephosphorylation
6    5 80        inhibition

KEGGgraph documentation built on Nov. 8, 2020, 5:42 p.m.