QTDT - Data File

This file describes the pedigree file organization. Each line in the data file includes two items, the first specifying a data type and the second a label. Each item corresponds to a successive column in the pedigree file.

Code	Description
M	Marker Genotype. In the pedigree file, marker genotypes are encoded as two integers, separated by a tab, space or a '/' (forward slash). Missing values should be encoded as 0 or using an appropriate text label such as x or NA.
T	Trait. In the pedigree file, quantitative phenotypes are encoded as numbers. Missing values should be encoded with an appropriate text label such as x or NA, although a numeric value such as -99.999 may also be used.
C	Covariate. In the pedigree file, covariates are encoded in the same manner as quantitative phenotypes.
Z	Zygosity. In the pedigree file this column encodes twin status. The following codes are recommended: zero indicating individuals who are not twins, MZ for monozygotic twins and DZ for dizygotic twins. For additional details see the twins section.
A	Affection status. Denotes a binary disease phenotype. In the pedigree file, disease status is commonly coded as 0 or x for unknown, 1 for unaffected and 2 affected.
S[n]	Skip column. Indicates that the corresponding column in the pedigree file should be discarded. To ignore consecutive columns, the subscript n may be specified - eg, S2 ignores the next two columns.

For example, if two polymorphisms in the growth hormone gene were investigated for association to height, and if age was used as a covariate, the corresponding data file might be:

 T    HEIGHT
 M    GH1_SNP132
 M    GH1_SNP146
 C    AGE

The pedigree file might look like this:

  1000 1 0 0 1  1.87  1/2 2/2  40
  1000 2 0 0 2  1.65  1/2 1/1  38
  1000 3 0 0 1  1.80  1/1 1/2  20
  1000 4 0 0 1  1.75  2/2 1/2  17
  (...)