topPathways: Retrieve top pathways

View source: R/topPathways.R

topPathwaysR Documentation

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")


cannin/paxtoolsr documentation built on Feb. 2, 2023, 11:44 a.m.