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INSTALL_ME.txt
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INSTALL_ME.txt
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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-4.4.1-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_1.68.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_1.68.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-4.4.1.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_1.68.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_1.68.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_1.68.tar.gz
You'll probably need to be superuser.
b. To install the package locally, type
R CMD INSTALL --library=/home/auser/Rlibs qtl_1.68.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 <[email protected]>.
----------------------------------------------------------------------
end of INSTALL_ME.txt