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.
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.
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.
Covariate. In the pedigree file, covariates are encoded
in the same manner as quantitative phenotypes.
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
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
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:
The pedigree file might look like
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