QTDT - Online Documentation
Speeding up analysis of SNP markers
By default, QTDT analyses every allele at every marker locus.
For di-allelic markers, both alleles will provide exactly the
same evidence for association. When analysing sets consisting
solely of biallelic markers (such as SNPs), you may wish to specify
that you only want to analyse one allele at each marker. This
will reduce the amount of output and may even speed things up
a bit:
prompt> qtdt --snp
Parent-of-origin effects
For total association or transmission disequilibrium tests with the
orthogonal model, the effects of maternally and paternally derived alleles
may be modelled separately by specifying the -o option:
File |
Description |
-ot |
Tests whether maternal and paternal alleles are significantly
different |
-of |
Uses a saturated model, where paternal and paternally inherited
alleles are modelled separately |
-om, -op |
Test only maternally or paternally derived alleles. |
When the imprinting option is requested the informative individuals are two groups of informative individuals. One
group is always included in analyses, the other group is only included when testing association at the population level
(-at option, which does not control for population stratification):
The first group includes those individuals where both parents are genotyped and where one parent is homozygous or
the mother and father have different genotypes. In addition, when paternal imprinting is tested, the father must be
heterozygous and, when maternal imprinting is tested, the mother must be heterozygous. When the effects of maternal
and paternal alleles are modelled simultaneously, at least one parent must be heterozygous.
The second group includes all individuals with at least one homozygous parent. In this group, genotypes for the
other parent may be missing. This group is only included when testing effects of imprinting at the population
level.
For example, to test whether there are differences between maternal and paternal alleles:
prompt> qtdt -ao -ot
If you find significant differences you may then wish to consider
the saturated model:
prompt> qtdt -ao -of
Ridiculously Brief Description of Output
QTDT outputs a short description of the linear and variance
models that will be considered for both the null and alternative
hypothesis, before running any tests.
For each test run, a brief summary including likelihood/goodness-of-fit
statistics, number of informative individuals, and p-value (if
<= 0.10) is output.
The regression tables file (regress.tbl by default), includes
additional information including parameter estimates under the
null and alternative hypothesis.
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