The R-package proteomics

Introduction

This is an R-package for the Statistical Analysis of High Throughput Proteomics Data. The package provides methods for making inference in isobaric labelled LC-MS/MS experiments, namely iTRAQ experiments. It provides a function that reasonably parses a CSV-export from Proteome Discoverer(TM) into a data frame that can be easily handled in R. Functions and methods are provided for quality control, filtering, norming, and the calculation of response variables for further analysis. The merging of multiple iTRAQ experiments with respect to a reference is also covered.

Installation from CRAN

The easiest way to install the package in a running R environment is:

install.packages("proteomics")
library("proteomics")

Installation manually from GitHub

After cloning the repository, you may use the following magic in the build directory to build and install the package on your system:

make package
make install

Then open up an R-session and type:

library("proteomics")

And you are good to go.

Where to start

A small tutorial will be soon appearing here.

Author

Thomas W. D. Möbius (kontakt@thomasmoebius.de)