Saunak Sen

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R/qtlDesign: Software for QTL experimental design

About R/qtlDesign is software to help plan quantitative trait locus (QTL) experiments. It is an add-on library of functions to the R programming language. The current version is 0.91.

Disclaimer The source code and software distributed in this web page has no express or implied warranty. Use at your own risk.

Download On computers where a R GUI is available (Mac OS X and Windows), you may find it convenient to install via the graphical "Package installer" located in the "Packages and Data" menu.

The following steps will work if the graphical interface is unavailable or broken for some reason.

Start up R. If you do not have R, you have to install it first.
Choose a CRAN mirror (download site). It is usually best to choose a location that is geographically closet to you. Type into the command window:
```
chooseCRANmirror()
```
If this does not work for some reason use
```
chooseCRANmirror(graphics=F)
```
Download and install the package. Use:
```
install.packages("qtlDesign",type="source")
```
If you do not have administrative privileges on your computer, you will have to choose a directory where you have write permissions. For example, Mac OS X users may do something like:
```
install.packages("qtlDesign",lib="/Users/john/Rlibs",type="source")
```
which means that package will be installed in the directory "Rlibs" of the user "john" (assuming you are "John"). Choose a directory with a different name than "Rlibs" if you like. Windows users can similarly specify a directory. It will look something like "c:\john\rlibs".
Load the package. You have to do this every time you start R and want to use the package.
```
library(qtlDesign)
```
If you installed the library into a non-system directory, then you have to specify the location of the library. For example, if you do not have administrative privileges and installed the library in "/Users/john/Rlibs", then you would enter
```
library(qtlDesign, lib.loc="/Users/john/Rlibs")
```

Users more comfortable with the command line may install the from source via a command line interface by downloading this file: qtlDesign_0.91.tar.gz. Then inside a shell window type:

R CMD INSTALL qtlDesign_0.91.tar.gz

R CMD INSTALL --library="/Users/john/Rlibs" qtlDesign_0.91.tar.gz

if you don't have administrative privileges on your computer and have to install in a user directory ("/Users/john/Rlibs" in this example).

Help Our paper gives an overview of the software and the theory underlying it. The software manual lists the functions and their usage.
When you have R installed, you can get a list of the functions by typing

library(help=qtlDesign)

library(help=qtlDesign,lib="/Users/john/Rlibs")

if R/qtlDesign is installed in the library "/Users/john/Rlibs".
Each function has its own help. For example, if you want help on the function

powercalc you can type ?powercalc  And please do not hesitate to email me
(sen@biostat.ucsf.edu) if you find bugs or have questions or comments.

...last updated 17 may 2007...