makeSPIAdata {SPIA} | R Documentation

## 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.

### Author(s)

Adi Laurentiu Tarca <atarca@med.wayne.edu>

### 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]

[Package SPIA version 2.39.0 Index]