paxtoolsr (version 1.6.3)

graphPc: 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

concept

paxtoolsr

See Also

pcFormats, pcDirections

Examples

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