toSif: Convert a BioPAX OWL file to SIF

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

Description

Convert a BioPAX OWL file to a binary SIF file

Usage

toSif(inputFile, outputFile = NULL)

Arguments

inputFile	a string of the name of the input BioPAX OWL file
outputFile	a string of the name of the output SIF file (Optional)

Details

Information on SIF conversion is provided on the Pathway Commons site: http://www.pathwaycommons.org/pc2/

Value

see readSif()

Examples

  
outFile <- tempfile()
results <- toSif(system.file("extdata", "raf_map_kinase_cascade_reactome.owl", 
  package="paxtoolsr"), 
  outFile) 
  

Example output

Loading required package: rJava
Loading required package: XML
OpenJDK 64-Bit Server VM warning: Can't detect initial thread stack location - find_vma failed
2018-06-26 18:28:24,022 0    [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
Warning message:
system call failed: Cannot allocate memory 

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