TrendTDT Manual

 

 

 

version 1.0 beta

 

 

September 7, 2007

Introduction

TrendTDT is a program to perform trend-TDT, TDT_L/S, and TDT_max test for association studies on functional VNTRs.

Features of the program

• Can handle multiplex pedigrees
• missing genotypes allowed
• multiple markers allowed

 

File list

Files in the package

trendTDT_xxx               executable program

trnTDTpar.txt                 example of parameter file

trnTDTpre.txt                 example of pedigree data file

clrtdt.r                             R command file for conditional logistic regression analysis

Files created

<marker_name>.out       result files

trnTDTerr.txt                  error reports

trnTDTall.out                 p-value reports of all markers

 

Prefile format

Prefile is a genotype data file in pre-“makeped” LINKAGE format, except that it has a title line, and that two consecutive returns will end the data section (therefore, users can add comments to the end of file, after two returns). In the title line, the first 6 fields must be “fid iid fath moth sex aff”, following by marker names. There should be two columns for earch marker, and the same marker name should be present for each of these two columns in the title line. Fields can be divided by white spaces such as blanks or tabs.

 

Table 1: prefile format.

Column	Name on title line	Description	Format
1	Fid	Family ID	Strings without white space
2	Iid	Individual ID	Strings without white space
3	Fath	Father ID	Strings without white space
4	Moth	Mother ID	Strings without white space
5	Sex	Sex	0/1/2, representing unknown/male/female
6	Aff	Affection status	0/1/2, representing unkown/unaffected/affected
7 8 ...	Marker name	Marker genotypes	Integers. "0 0" represents unknown genotype.

Parameter file format

Parameter file is provided in the package. Users can modify this parameter file according to their own needs. The parameters include name of the prefile, the definition of risk alleles (whether shorter or longer alleles are risk alleles) and the definition of shorter/longer allele length (only for TDT_L/S test).

Usage of the program

This program is distributed as a “green software” (no need to install, no files copied into the system folder, such as c:/windows or c:/windows/system). To use the program, users can copy data file (pre-makeped LINKAGE format pedigree data file) to the program folder, modify the parameter file, then run the program (double click on the program icon in WINDOWS, or type “./trendTDT” in LINUX or Mac OS X). Result files will be created when finished. Please use common text editor programs or Microsoft EXCEL to read results.

 

This program will automatically create a file named "seed.txt". This file contains the seed for the random number generator in the next time this program runs. Random number is only used in simulations, not in trend-TDT, TDT_L/S, or TDT_max tests, so this seed will not affect the test results.

 

For conditional logistic regression analysis, R project need to be installed, and Path should be set to the "bin" directory of the R program. In addition, packages "splines" and "survival" are required.

 

Limitations

• When the result is very significant (p<10^-12), the p-value is simply shown as 0, and the –log(p) as +INF.
• This program can only check for Mendelian inconsistencies within each triad, more complicated misinheritance will not be detected. Therefore, before using this program, it is recommended to check for the genotyping errors by other softwares, such as PEDCHECK and MERLIN.

 

FAQs

o      It said something’s wrong in the pedigree structure, but I have checked my file and absolutely it has no error.
This may be caused by the different formats of the files in different operating systems, which make the program unable to recognize the "end of line". The solution to this is to use some third party software to change the format, such as flip (http://ccrma-www.stanford.edu/~craig/utility/flip/).