toSifnx: Converts BioPAX OWL file to extended binary SIF...

In BioPAX/paxtoolsr: Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Converts BioPAX OWL file to extended binary SIF representation

Description

Converts BioPAX OWL file to extended binary SIF representation

Usage

toSifnx(inputFile, outputFile = tempfile(), idType = "uniprot")

Arguments

inputFile	a string with the name of the input BioPAX OWL file
outputFile	a string with the name of the output file for SIFNX information
idType	a string either "hgnc" or "uniprot" (DEFAULT: uniprot, more common)

Details

Information on SIF conversion is provided on the Pathway Commons site: http://www.pathwaycommons.org/pc2/. Also, this is a Java-based methods, it is best to use full paths.

Value

see readSifnx()

Examples

inputFile <- system.file("extdata", "raf_map_kinase_cascade_reactome.owl", package="paxtoolsr")
results <- toSifnx(inputFile=inputFile) 

BioPAX/paxtoolsr documentation built on Jan. 31, 2023, 4:22 a.m.