INSTALL_ME file for the qtl package ---------------------------------------------------------------------- This explains the installation of the qtl package for R. If you have any problems with installation, send an email to Karl Broman . ---------------------------------------------------------------------- OBTAINING R You can download R from the Comprehensive R Archive Network (CRAN). Visit https://cran.r-project.org or a local mirror (for example, https://cran.rstudio.com). Source code is available for Unix, and binaries are available for Windows, MacOS, and many versions of Linux. OBTAINING R/QTL You can obtain the latest version of R/qtl from https://rqtl.org Copies of R/qtl will also be placed on CRAN (cran.r-project.org). Binaries are available for Windows and MacOS; source code is available for Unix. INSTALLATION OF R AND R/QTL (Windows) 1. The Windows version of R is distributed as a single file, with a name something like R-4.3.2-win.exe. Install R by executing this file. We recommend installing R in "c:\R" rather than "c:\Program Files\R". Why didn't Microsoft use "Programs" rather than "Program files"? 2. To install R/qtl, the simplest approach is to start R and type install.packages("qtl") This will download the binary from CRAN and install it. Alternatively, you can download the "qtl_1.64.zip" (or the equivalent). Then start R and select (on the menu bar) "Packages" and then "Install package from local zip file...". Find the file "qtl_1.64.zip" on your hard drive, and click "Open". INSTALLATION OF R AND R/QTL (MacOS version 10.13 and above) 1. Download the file R-4.3.2.pkg, double-click it, and follow the instructions. 2. To install R/qtl, the simplest approach is to start R and type install.packages("qtl") This will download the binary from CRAN and install it. Alternatively, download the compiled version of R/qtl for Mac OS X, a file like "qtl_1.64.tgz". Then start R and select (on the menu bar) "Packages & Data" -> "Package Installer". Select "Local Binary Package" from the drop-down menu at the top of the window that comes up. Click "Install" at the bottom of the window. Find the package on your drive and click "Open". Finally, close the window. INSTALLATION OF R/QTL (Unix) 1. We'll assume that R has already been installed. 2. To install R/qtl, the simplest approach is to start R and type install.packages("qtl") This will download the binary from CRAN and install it. Alternatively, download the R/qtl source code (a file like "qtl_1.64.tar.gz"). Go into the directory containing the file and do one of the following: a. To install R/qtl in the standard location (/usr/local/lib/R/library), type R CMD INSTALL qtl_1.64.tar.gz You'll probably need to be superuser. b. To install the package locally, type R CMD INSTALL --library=/home/auser/Rlibs qtl_1.64.tar.gz (where "/home/auser/Rlibs" should be replaced with the appropriate directory). Create a file ~/.Renviron containing the line R_LIBS=/home/auser/Rlibs so that R will know to search for packages in that directory. GETTING STARTED Once you start R, you'll need to type "library(qtl)" to load the package. You can create a file "~/.Rprofile" (Unix or MacOS) or "c:\.Rprofile" (Windows) containing R code to be run whenever you start R. If you use the R/qtl package regularly, you should place the line "library(qtl)" in such a file. Efficient use of the R/qtl package requires considerable knowledge of the R language. Learning R may require a formidable investment of time, but it will definitely be worth the effort. Numerous free documents on getting started with R are available on CRAN (https://cran.r-project.org). In addition, several books are available. For example, see WN Venables, BD Ripley (2002) Modern Applied Statistics with S, 4th edition. Springer. To get started with R/qtl, you might first peruse the documentation that is bundled with it. Type help.start() to start the html version of the R help pages. Then click "Packages" -> "qtl". In Windows or MacOS, you may gain access to the help documents by clicking "Help" in the menu bar and then "R language (html)". If you include "options(htmlhelp=TRUE)" in your .Rprofile file, use of the html version of the help pages will be automatic. The help file titled "A starting point" gives a brief walk-through of an example analysis, and so is a good place to start. You may also view this help file by typing ?"A starting point" from the command line in R. A tutorial on R/qtl (as a PDF document) is also available. It briefly describes the aims of the R/qtl package, lists the available functions grouped in categories, and provides a few extended examples. The tutorial is bundled with R/qtl, as "rqtltour.pdf" and is also available from the R/qtl website: https://rqtl.org CITING R/QTL To cite R/qtl in publications, use Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890 QUESTIONS/COMMENTS/CONCERNS If you have any questions, suggestions, problems or complaints regarding R/qtl, please email Karl Broman . ---------------------------------------------------------------------- end of INSTALL_ME.txt