Class | Analysis and data manipulation command |
Name | tdt |
Arguments | <binary trait>|<quantitative trait> [>|>=|<|<=|==|^= <threshold>] [cutoff <cutoff>] [mat|pat] |
Prints transmission-disequilibrium statistics for all marker loci versus the trait, where an index person is either affected with a binary trait, or whose value for a quantitative trait exceeds the given threshold. Since binary traits are coded internally as 2=y and 1=n, an analysis using unaffecteds as proband can be performed as tdt <binary trait> under 2. Similarly, in unascertained families, tdt <binary trait> over 0 tests for segregation distortion.
For quantitative traits, either a threshold can used to dichotomize phenotypes, or a QTDT due to Gauderman [2003] can be performed.
Calculation of the TDT statistic can be restricted to pairs of cells whose total is greater than cutoff, eg 5, and to the maternal or paternal contributions, if parent-of-origin effects are suspected.
Example:
>> tdt adjChol ------------------------------------------------ TDT for trait "adjChol" v. all markers ------------------------------------------------ ------------ QTDT for "ldl "------------- Allele Allelic Mean Stand Error Count ----------------------------------------------- 1 29.1111 33.5686 24 2 244.5556 33.5686 6 ---------------------------------------------- Total 196.6667 118.3860 30 No. trait(+) marker(-) = 0 No. trait(+) marker(+) = 15 No. marker mating types = 2 Allelic Mean Square = 104436.6944 (df= 1) Residual Standard Error = 76.1265 (df= 12) F-Statistic = 18.0211 Nominal P-value = 0.0011 Equalled or exceeded by = 1/ 201 simulated values (0.0050)
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