SEMgraph (version 1.2.4)

loadPathways: Import pathways and generate a reference network

Description

Utility to create pathway lists as igraph objects and interaction networks from Reactome, KEGG, and other pathway databases.

Usage

loadPathways(db, organism = "hsapiens", id_type = "ENTREZID", lcc = TRUE, ...)

Value

A list of 2 objects:

1. a list of pathways ad igraph objects;

2. the union of graphs in the pathway list.

Arguments

db

String indicating the database name. Please, check the pathways function from graphite to list the available datasets.

organism

A string indicating the source organism. Please, check the pathways function from graphite to list the available datasets (default = "hsapiens")

id_type

Gene ID type. The default is set to "ENTREZID" (standard SEM fitting nomenclature). A common choice could be "SYMBOL", for official gene symbols.

lcc

A logical value. If TRUE (default), the reference network will only include the largest connected component. It will include all disconnected components otherwise.

...

Currently ignored.

Author

Fernando Palluzzi

Details

This function uses graphite to download and preprocess network data from pathway databases. The output is then created using igraph and SEMgraph utilities.

References

Sales G, Calura E, Cavalieri D, Romualdi C (2012). graphite - a Bioconductor package to convert pathway topology to gene network. BMC Bioinformatics. <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-20>

Examples

if (FALSE) {

# Create KEGG reference pathway list and reference network for Homo sapiens
kegg.hs <- loadPathways("kegg", "hsapiens", "ENTREZID")

# Inspect results
names(kegg.hs$pathways)
kegg.hs$network

}