example 6

Example 6 - A series of single-marker association studies using EH+ :

motivation

One option in EH ( web ) or EH+ (also FASTEH+ ) ( web ) program is to compare the allele frequencies of a marker in case group (patients taken randomly from the population) and control group (normal, unaffected persons taken randomly from the population). This association study sometimes is repeated for many markers. We would like to automate this repetition.
set up

You need to have EH+ or FASTEH+ program installed on your computer (source is at http://www.iop.kcl.ac.uk/IoP/Departments/PsychMed/GEpiBSt/software.stm ). The particular program we use in this Perl script is fpmp (fast, permutation-test, model-free, plus) in FASTEH+.
You have to have a .dat file (first column indicates person ID; second column indicates affection status: 0 for control, 1 for case; then each two subsequent columns contain genotype of one marker: one of the columns is the allele derived from the mother, and another is the allele derived from the father, although the order of the two is unknown so exchangeable).
To run fpmp, a .par file is also required. But our perl script will prepare this file.
the Perl script (ehplus_cc.pl) that runs fpmp in FASTEH+ for each marker in the genotype data in .dat file.

This is a companion page for W Li, F Haghighi, "Perl as a tool for linkage analysis", American Journal of Human Genetics, supplement to vol 65, page A260 (1999) (poster number 1452 at the Annual Meeting of American Society of Human Genetics 1999, San Francisco, CA)