graphPc {paxtoolsr} | R Documentation

## Get Pathway Commons BioPAX elements

### Description

This function will retrieve a set of BioPAX elements given a graph query match.

### Usage

    graphPc(kind, source, target = NULL, direction = NULL, limit = NULL,
      format = NULL, datasource = NULL, organism = NULL, verbose = FALSE)

### Arguments

`kind` | graph query. Valid options can be found using `pcGraphQueries` See Details for information on graph queries.
`source` | source object's URI/ID. Multiple source URIs/IDs are allowed per query, for example c("http://identifiers.org/uniprot/Q06609", "http://identifiers.org/uniprot/Q549Z0") See a note about MIRIAM and Identifiers.org in details
`target` | [Required for PATHSFROMTO graph query] target URI/ID. Multiple target URIs are allowed per query; for example c("http://identifiers.org/uniprot/Q06609", "http://identifiers.org/uniprot/Q549Z0") See a note about MIRIAM and Identifiers.org in details
`direction` | [Optional, for NEIGHBORHOOD and COMMONSTREAM algorithms] - graph search direction. Valid options: `pcDirections`.
`limit` | graph query search distance limit (default: 1).
`format` | output format. Valid options: `pcFormats`
`datasource` | datasource filter (same as for 'search').
`organism` | organism filter (same as for 'search').
`verbose` | a boolean, display the command used to query Pathway Commons

### Value

depending on the the output format a different object may be returned. `pcFormats`

### See Also

`pcFormats, pcDirections`

### Examples

    source <- "http://identifiers.org/uniprot/O14503"
    #results <- graphPc(source=source, kind="neighborhood", format="TXT")

[Package paxtoolsr version 1.18.0 Index]