Jurg Ott
Institute of Psychology, CAS, Beijing
Rockefeller University, New York
9 Jan 2012
Instructions for the use of the FP test
The theory of this association test may be found in the
manuscript listed below (Zhang et al 2008). Download the program
package (FPtest.zip) and
move its
contents into a folder. Preferably, run the FPtest program in a Windows
command window (CMD), or double-click on FPtest (FPtest.exe).
The program will compute p-values via permutation samples, with the
observed data being counted as a null dataset. Thus, the smallest p-value
that can be obtained is 1/n,
where n is the number of permutations performed.
Choose a suitably large number of permutation samples such as 20,000 or
more. The program will write output to a file called FPtestout.txt.
Reference for sample data
Zhang Q, Wang S, Ott J. Combining identity by descent and and
association in genetic case-control studies. BMC Genetics 2008,
9:42