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Last data update: 2014.03.03

R: Process KGML files for spia analysis

makeSPIAdata

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>

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]

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(SPIA)
Loading required package: KEGGgraph

Attaching package: 'KEGGgraph'

The following object is masked from 'package:graphics':

    plot

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SPIA/makeSPIAdata.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makeSPIAdata
> ### Title: Process KGML files for spia analysis
> ### Aliases: makeSPIAdata
> ### Keywords: nonparametric methods
> 
> ### ** Examples
> 
> library(SPIA)
> data(colorectalcancer)
> makeSPIAdata(kgml.path=system.file("extdata/keggxml/hsa",package="SPIA"),organism="hsa",out.path="./")
[1] TRUE
> res<-spia(de=DE_Colorectal, all=ALL_Colorectal, organism="hsa",data.dir="./")

Done pathway 1 : RNA transport..
Done pathway 2 : Progesterone-mediated oocyte m..
Done pathway 3 : Colorectal cancer..> res[,-12]
                                     Name    ID pSize NDE       pNDE       tA
1                       Colorectal cancer 05210    57  24 0.04319608 8.518932
2 Progesterone-mediated oocyte maturation 04914    77  29 0.11159960 2.510327
3                           RNA transport 03013   141  31 0.99138776 0.000000
  pPERT          pG      pGFdr     pGFWER    Status
1 0.029 0.009623719 0.02887116 0.02887116 Activated
2 0.608 0.250404319 0.37560648 0.75121296 Activated
3 1.000 0.999962808 0.99996281 1.00000000 Inhibited
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>