Retrieve top pathways

Description

This command returns all "top" pathways.

Usage

1
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

Details

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

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

Examples

1
2
datasource <- "panther"
#results <- topPathways(datasource=datasource)

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