lect 16.2 - Introduction to R and Bioconductor Introduction...

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Introduction to R and Bioconductor Introduction to the R language Countway Library, Sept 2009, Aedin Culhane ([email protected]) I R Background Why is it called R? The name is partly based on the (first) names of the first two R authors (Robert Gentleman and Ross Ihaka), and partly a play on the name of the Bell Labs language ‘S Short R History 1991: Ross Ihaka and Robert Gentleman begin work on a project that will ultimately become R 1993: The first announcement of R 1995: R available by ftp 1996: A mailing list is started and maintained by Martin Maechler at ETH 1997: The R core group is formed 1998: The Omega project began in July 1998. The aim of the project was to develop software to enable the statistical computing languages, S, R, and Lisp-Stat work with web-based software and Java, the Java virtual machine and other programming languages. 2000: R 1.0.0 is released 2001: Bioconductor, an open source and open development software project for the analysis and comprehension of genomic data, using R started in Fall 2001. 2008: R current release is version 2.9.2 which was released on 2009-08-24. There are normally 2 releases a year, April and October. (R 2.9.0 was released in April). 2008: Bioconductor, current release is version 2.4 (released April, 2009). This release is designed for R 2.9. Bioconductor coincide and follow R release. 2008: The Omegahat project contains code to enable connectivity between R and Java, XML, perl, python, cURL/SSOAP, xLISP and some functions that talk to Matlab, and SAS. R environment extensive, coherent, integrated collection of tools for data analysis language for expressing statistical models effective data handling and storage facility 1
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a suite of operators for calculations on matrices graphical facilities for data analysis and display (computer screen and/or hardcopy) a programming language including conditionals, loops and input/output facilities extended rapidly by a large collection of packages . II Obtaining and managing R R can be downloaded from the website: http://cran.r-project.org/ . See additional notes which give a very detailed description on downloading and installing R (and Bioconductor). R is available for all platforms: Unix/Linux, Windows and Mac. In this course, we will concentrate on the Windows implementation. The differences between the platforms are minor, so most of the material is applicable to the other platforms. II.1 Useful related software: An alternative to the standard R interface, is RCMDR http://socserv.mcmaster.ca/jfox/ Misc/Rcmdr/ , it has a few more drop down menus and buttons than the standard R in win- dows. For a more complete list of graphical user (point and click) interfaces for R, that are in development see http://www.sciviews.org/ Editors (which color your code) for R, include Tinn-R http://www.sciviews.org/Tinn-R/ , WinEdt text editor, and ESS (Emacs speaks statistics) http://ess.r-project.org/ . On Linux, I like to use Kate http://kate.kde.org/ Nice editors for LaTeX include Texmacs http://www.texmacs.org a WYSIWYG editor for TeX and Texmaker http://www.xm1math.net/texmaker/ III Becoming familiar with the default R
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