getPc: Get Pathway Commons BioPAX elements

Description Usage Arguments Details Value See Also Examples

View source: R/getPc.R

Description

This command retrieves full pathway information for a set of elements such as pathway, interaction or physical entity given the RDF IDs.

Usage

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getPc(uri, format = "BIOPAX", verbose = FALSE, ...)

Arguments

uri

a vector that includes valid/existing BioPAX element's URI (RDF ID; for utility classes that were "normalized", such as entity refereneces and controlled vocabularies, it is usually a Idntifiers.org URL. Multiple IDs are allowed per query, for example, c("http://identifiers.org/uniprot/Q06609", "http://identifiers.org/uniprot/Q549Z0") See also about MIRIAM and Identifiers.org in details.

format

output format (Default: BIOPAX). Valid options can be found using pcFormats

verbose

a boolean, display the command used to query Pathway Commons

...

additional arguments to read* methods that handle data from Pathway Commons

Details

Get commands only retrieve the BioPAX elements that are directly mapped to the ID. Use the "traverse query to traverse BioPAX graph and obtain child/owner elements.

Information on MIRIAM and Identifiers.org http://www.pathwaycommons.org/pc2/#miriam

Value

a XMLInternalDocument object

See Also

pcFormats

Examples

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uri <- "http://identifiers.org/uniprot/O14503"
#results <- getPc(uri)

uri <- c("http://identifiers.org/uniprot/O14503", "http://identifiers.org/uniprot/Q9P2X7")
#results <- getPc(uri, verbose=TRUE)

cannin/paxtoolsr documentation built on Jan. 13, 2018, 4:53 p.m.