graphPc: Get Pathway Commons BioPAX elements

View source: R/graphPc.R

graphPcR 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")


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