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

Description Usage Arguments Details Value Examples

View source: R/toSifnx.R

Description

Converts BioPAX OWL file to extended binary SIF representation

Usage

1
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

1
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inputFile <- system.file("extdata", "raf_map_kinase_cascade_reactome.owl", package="paxtoolsr")
results <- toSifnx(inputFile=inputFile) 

cannin/paxtoolsr documentation built on Aug. 16, 2018, 1:18 a.m.