Sib-pair Command: tdt

ClassAnalysis and data manipulation command
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.


>> 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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