PedGenie / QTDT Interface Home PageΒΆ
PedGenie interfaces with the freely available QTDT statistical package to run the following quantitative transmission disequilibrium tests TDTQ5 (Allison 1997), (Rabinowitz 1997), and (Monks et al 1998). These traditional statistical tests typically allow only a single trio or a single sibship to be present in a kindred. PedGenie allows multiple trios and/or multiple sibships to be present in a kindred, as well as multiple affected/unaffected siblings to be present within a family. By generating an empirical p-value that corrects for familial correlations, PedGenie is able to handle pedigrees of any size. PedGenie communicates the real data and each simulation to the QTDT package, and an empirical p-value is calculated. The QTDT package contains other tests, such as (Abecasis et al. 2000) and (Fulker et al 1999) as part of the package, but these tests require an inherited-by-descent (IBD) file to generate valid results. As PedGenie does not utilize an IBD file, interfacing with these tests is not recommended.
- Execute PedGenie to create TDT Dump files
- Run each of the dump files thru the modified QTDT program to produce a single output file.
- Execute the Pval package with the modified QTDT output file.
Output Report
Output Report will be written to [Pedigree file name].[rgen parameter file name].out.pval
Development Software
This QTDTpval package was developed in Java version 1.4.