keggPathwayGraphs {ROntoTools} | R Documentation

## Download and parse KEGG pathway data

### Description

Download and parse KEGG pathway data

### Usage

    keggPathwayGraphs(organism = "hsa", targRelTypes = c("GErel", "PCrel",
      "PPrel"), relPercThresh = 0.9, nodeOnlyGraphs = FALSE,
      updateCache = FALSE, verbose = TRUE)

### Arguments

`organism` | organism code as defined by KEGG
`targRelTypes` | target relation types
`relPercThresh` | percentage of the number of relation types over all possible realtions in the pathway
`nodeOnlyGraphs` | allow graphs with no edges
`updateCache` | re-download KEGG data
`verbose` | show progress of downloading and parsing

### Value

A list of `graphNEL` objects encoding the pathway information.

### Author(s)

Calin Voichita and Sorin Draghici

### See Also

`keggPathwayNames`

### Examples

    # The pathway cache provided as part of the pathway contains only the
    # pathways that passed the default filtering. We recommend, re-downloading
    # the pathways using the updateCache parameter
    kpg <- keggPathwayGraphs("hsa")

    # to update the pathway cache for human run:
    # kpg <- keggPathwayGraphs("hsa", updateCache = TRUE)
    # this is time consuming and depends on the available bandwith.

    head(names(kpg))

    kpg[["path:hsa04110"]]
    head(nodes(kpg[["path:hsa04110"]]))
    head(edges(kpg[["path:hsa04110"]]))

[Package ROntoTools version 2.12.0 Index]