topPathways: Retrieve top pathways

In BioPAX/paxtoolsr: Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Retrieve top pathways

Description

This command returns all "top" pathways.

Usage

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

Arguments

q	[Optional] a keyword, name, external identifier, or a Lucene query string, like in 'search', but the default is '*' (match all).
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

#results <- topPathways(q="TP53", datasource="panther")

BioPAX/paxtoolsr documentation built on Jan. 31, 2023, 4:22 a.m.