SPIA (version 2.24.0)

makeSPIAdata: Process KGML files for spia analysis

Description

This function processes KEGG xml files into a xxxSPIA.RData file needed for spia function.

Usage

makeSPIAdata(kgml.path="./hsa",organism="hsa",out.path=".")

Arguments

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.

See Also

spia

Examples

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]