topPathways {paxtoolsr} | R 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")

[Package paxtoolsr version 1.26.0 Index]