graphPc: Get Pathway Commons BioPAX elements

In paxtoolsr: PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons

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")

paxtoolsr documentation built on Nov. 8, 2020, 8:29 p.m.