paxtoolsr (version 1.6.3)

topPathways: Retrieve top pathways

Description

This command returns all "top" pathways.

Usage

topPathways(datasource = NULL, organism = NULL, verbose = FALSE)

Arguments

datasource

filter by data source (same as for 'search').

organism

organism filter (same as for 'search').

verbose

a boolean, display the command used to query Pathway Commons

Value

• a data.frame with the following columns:
  • uri URI ID for the pathway
  • biopaxClass the type of BioPAX object
  • name a human readable name
  • dataSource the dataSource for the pathway
  • organism an organism identifier
  • pathway URI ID for the pathway

concept

paxtoolsr

Details

Pathways that are neither 'controlled' nor 'pathwayComponent' of another process.

Examples

datasource <- "panther"
#results <- topPathways(datasource=datasource)