SUMO - - Run R-scripts

SUMO - Run R-scripts

R is a powerful open source statistical evaluation platform offering a large variaty of preset statistical tools.
Originally, R is operated via a command line which is sometimes complicated to use.

Therfore, a few R functions are wrapped by SUMO, allowing an unexperienced user to setup and run complicated statistical tests without deeper knowledge and experience of R.

Required is a functional R installation.

Donwload and install R.

Under Windows7 there may be a problem:

R is installed in Windows' program folder (e.g. "c:\program files\r\rxxxx\...").
but windows shows and uses a symbolic link to this folder (e.g. c:\programme\r\rxxxx\...
R-GUI is working correctly, but sometime the scriptable command lines version of R doesnt work properly (e.g. R doesn't find the default packages).

In such cases check that the path to R is correctly set in the Windows path environment variable or install R outside Window' program folders (e.g. create a "d:\programs" folder and install R there).

Install packages

R is a general purpose development environment, offering a large set of basic mathematical and statistical fuctions.

Special applications may require additonal functions, or R-scripts
One way to supply such functionality is to generate und publish "packages" - a combination of R-scrpts, data, documentation and extensions of R.

To install such packages, start R and use the R-console:

Type a command and press ENTER-key.
R will try to execute the requested function - or write an error message.

In the example you can see the command how to installe the survival package, required to e.g. execute cox regression.
R might ask you for a mirror site: select the geographically closest to your location (in Germany e.g. Münster).

Presently SUMO wraps functions from packages:

Package	Function / Application
survival	coxph - Cox regresson
cophw	cophw - Weighted Cox regresson
illuminaio	Extract intensity data from Illumna IDat files
RPPM	BMIQ normalistation script for methylation data
minfi	funnorm - Normalisation of methlation data
sva	combat - batch compensation

Analyze problems with R-wrapper

Most functions within SUMO which wrap R-functions show you the r-script.
In case of fundamental problems with suc functions, it might be helful to copy the generated R-scripts into the R-console and analyze any problems.