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les package: Identifying Differential Effects in Tiling Microarray Data

Table of Contents

Summary

The les package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.

Authors: Julian Gehring, Clemens Kreutz, Jens Timmer
Maintainer: Julian Gehring <julian.gehring (at) fdm.uni-freiburg.de>

Availability, source code, and licensing

The les package is written for R and part of the bioconductor project since the 2.7 release in October 2010. This provides the latest stable release version and the current developer version, including builts for major platforms supported by R.

The complete source code of the package is publically accessible at github and licenced under the General Public License version 3 (GPL-3). You are free to use the software for any purposes and you are also welcome to contribute to it in any way.

Usage

Installation

In order to install the latest stable version of the les package from the bioconductor repository, simply run in your R session:

   source("http://bioconductor.org/biocLite.R")
   biocLite("les")

Alternatively, you can also obtain the built packages from bioconductor and install them manually:

   install.packages("path/to/les_x.y.z")

Please note that the first method is generally the best choice.

Loading the package

After the package has been installed, you can load it:

   library(les)

Documentation

A comprehensive example session on how to analyze gene sets with the les package can be found in the vignette of the package. This can also be assessed as a pdf file from the bioconductor website or within R:

   vignette("les")

Detailed descriptions of the objects, functions, and their parameters are provided in the help pages. For details about individual parts, e.g. the estimate method, you can read the help file within R:

   ?estimate

Contact and contribution

If you have any questions, comments, or contributions:

Date: 2011-08-05 22:42:09 CEST

Author: Julian Gehring