topPathways {paxtoolsr} | R Documentation |
This command returns all "top" pathways.
topPathways(datasource = NULL, organism = NULL, verbose = FALSE)
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 |
Pathways that are neither 'controlled' nor 'pathwayComponent' of another process.
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
datasource <- "panther" #results <- topPathways(datasource=datasource)