TrendTDT Manual

 

 

TrendTDT Manual

 

 

 

version 1.0 beta

 

 
September 7, 2007

Introduction

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

Features of the program

 

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 TDTL/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, TDTL/S, or TDTmax 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

 

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/).

 

 

 

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