toSifnx: Converts BioPAX OWL file to extended binary SIF...
In cannin/paxtoolsr: Access Pathways from Multiple Databases Through BioPAX and Pathway Commons
toSifnx R Documentation
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)
cannin/paxtoolsr documentation built on Feb. 2, 2023, 11:44 a.m.
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| toSifnx | R Documentation |
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)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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