makeSPIAdata {SPIA} | R Documentation |
This function processes KEGG xml files into a xxxSPIA.RData file needed for spia function.
makeSPIAdata(kgml.path="./hsa",organism="hsa",out.path=".")
kgml.path |
Character vector giving the location of the folder containing two or more KEGG xml files. See for e.g. http://www.genome.jp/kegg/pathway/hsa/hsa04010.html and click the Download KGML to get such files. Users that have a license to the KEGG ftp directory can copy all the xml files corresponding to a givne organism. |
organism |
A three letter character designating the organism. See a full list at ftp://ftp.genome.jp/pub/kegg/xml/organisms. |
out.path |
Directory where a "organism"SPIA.RData file will be saved. If left to null, it will will try to save the file in th extdata folder of the SPIA library. |
Adi Laurentiu Tarca <atarca@med.wayne.edu>
library(SPIA) data(colorectalcancer) makeSPIAdata(kgml.path=system.file("extdata/keggxml/hsa",package="SPIA"),organism="hsa",out.path="./") res<-spia(de=DE_Colorectal, all=ALL_Colorectal, organism="hsa",data.dir="./") res[,-12]