Overview
SFDR is a program to compute FDR q-values of genome-wide SNP association analysis within each stratum. Especialy the SFDR program is taylored to directly use genome-wide linkage scan results to assign strata. Weighted FDR q-values can be also computed as an alternative to SFDR. To understand the details of FDR, SFDR and WFDR control methods, see references at the bottom. Also, you can find a breif introduction of the methods in the the program manual document here.
Program Download
Download following files:
- SFDR.pl: SFDR program Perl script
- SFDR.exe: SFDR program executive file for Windows
- SFDR.pdf : Program manual
How to run a Perl script program
Perl is a script language. Once you install an Perl interpreter program in your computer, you don't need to compile and create separte executive file. By running the script file itself or calling the Perl interpreter for the script, it automatically compiles and runs the program.
- UNIX or LINUX Systems: Most of LINUX or UNIX systems usually have Perl interpreter istalled already. In that case, you can run a Perl script file *.pl by typing the file name and entering (some systems require "./" infront of it). Perl will recognize it. The UNIX or LINUX system will recognize the perl scrip by the first line of the file, which is a path directory starting by '#!'(for example : "#!/usr/bin/perl") . This is the indicator for the path where the Perl is installed. If your UNIX or LINUX system has different path for Perl, change the header accordingly. To find out the correct path for Perl, you may ask your system administrator.
- WINDOWS : Go to the command line window where the script file (MS-DOS mode). If you installed Perl interpreter, You may need to type "perl" before the Perl script file. For example, "perl example.pl".
How to obtain and install a Perl Interpreter
If you want a Perl interpreter installed, go to http://www.perl.org/get.html. You can download a Perl interpreters for your OS system.
Also, I strongly recommend Strawberry Perl at http://strawberryperl.com for Windows users (32 and 64 bit).
References
FDR - Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B. 57, 289-300 (1995)
q-value - Storey, J.D. A direct approach to false discovery rates. J. R. Stat. Soc. B.64, 479-498 (2002)
SFDR - Sun, L., Craiu, R.V., Paterson, A.D. & Bull, S.B. Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies. Genet. Epidemiol. 30, 519-530 (2006)
WFDR - Roeder, K., Bacanu, S.A., Wasserman, L. & Devlin, B. Using linkage genome scans to improve power of association in genome scans.Am. J. Hum. Genet. 78, 243-252 (2006)
We are planning to update our program regularly. You are welcome to suggest features that you want us to implement into this program. We greatly appreciate if you could point out any bugs when you use our program to :
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Lei Sun Dalla Lana School of Public Health Department of Statistics University of Toronto Phone: (416) 978-7519 E-mail: sun at utstat dot toronto dot edu Homepage: http://www.utstat.toronto.edu/sun/ |
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Yun Joo Yoo Samuel Lunenfeld Research Institute Mount Sinai Hospital, Toronto Phone: (416) 586-4800 ext 5836 E-amil: yoo at mshri do on dot ca Homepage: http://www.mshri.on.ca/yoo |
Last Updated Date: Nov 10, 2008