BayesMendel Lab

Older versions of the BayesMendel R package are described below and available by email request. Please send your name, institution, and package version number desired to bayesmendel@jhu.edu

Updates	Version
Improved output description (documentation) Fixed the problem with endometrial cancer in CRCAPRO	1.1-15
Added in new BRCA penetrances for AJ and nonAJ (Chen 2004) BRCApenet.AJ.2004 BRCApenet.nonAJ.2004 Updated HNPCCpenetrance penet.2004 Impoved documentation for the penetrance objects	1.2-1
Added in MakeRelationship.R Added in BRCApenet.Italian.RData, the BRCA penetrance object for the Italian population (Marroni 2004) Added in Australian.R (Apicella 2003) Improved the documentations	1.2-2
Updated BRCApenet.AJ.2004 and BRCApenet.nonAJ.2004	1.2-3
Fixed a bug in cancerrisk.R	1.2-4
Fixed a typo in brcapro.R (It does not affect the calcuation though) Added a patch (margenerec.c) so that BayesMendel can handle models with recessive mode of inheritance. See the help file for aveG(), which can now be specified to do recessive calculations. Replace Australian.R with LAMBDA.R, use the help file for LAMBDA() for details.	1.2-5
Updated penetrance estimates for breast and ovarian cancers Oophorectomy history can be included in the model Molecular marker information can be included in the model	1.3-1
Added generic 'plot' option to display pedigree structure and probabilities	1.3-2

First time R users:

If R is not installed on your computer, you need to install it before you can use BayesMendel. R is free and open source and available at the CRAN website. Once you get there, if you use Windows, click on "Windows (95 and later)" then click on "base" then click on "rw1091.exe" this will start the download. Once you have the exe file, click on it and it will install. Once installed, click to start.If you use linux or a mac, you probably know what to do once you get to CRAN.

At this point the best thing to do is to spend a day or two familiarizing yourself with R. In addition to the extensive materials provided at CRAN, a couple of very good places to get a quick start are the Statistical Computing Class at JHSPH or the R course by Bates and Lumley. Among the things you will learn is how to install a package (it's an easy thing to do). BayesMendel installs like any other package.

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