[R] Incomplete Trio in TDT analysis

[Farrel Buchinsky]

I am involved in a study where, as in most of life, men demonstrate
themselves to be recalcitrant. So while we have many probands and most of
their mothers we only have about 50% of the trios being complete.

I have been running tdt and trio.types. It appears as if it is ignoring the
duos. Sometimes a duo can be informative. For instance
Father ..missing
Mother 1/2
Proband 1/1
This duo shows that for allele 2, this was clearly a case where 2 was
untransmitted. 
Yet I do not think this family counts toward the output that is generated.
Am I correct? How do I use R to do TDT analysis where duo's are used if they
are informative?

If you want further details...

I made a subset that I called MessWith and it is made up of the first 24
probands and their parents. 2 probands had neither a mother nor a father. Of
the remaining, probands, 16 only had one parent.
> summary(Genotype.914186)

Number of samples typed: 52 (72.2%)

Allele Frequency: (2 alleles)
   Count Proportion
1     73        0.7
2     31        0.3
NA    40         NA


Genotype Frequency:
    Count Proportion
1/1    26        0.5
1/2    21        0.4
2/2     5        0.1
NA     20         NA

Heterozygosity (Hu)  = 0.4225168
Poly. Inf. Content   = 0.3309022

tdt(Genotype.914186, MessWith, famid, pid, fatid, motid, sex, affected )
        Transmission/disequilibrium test
Data:   Genotype.914186

Untransmitted allele frequencies, informative transmissions
and exact P-values

       Allele     Frequency   Transmitted Untransmitted       P-value 
            2        0.3333             3             2         1.000 

trio.types(Genotype.914186, MessWith, famid, pid, fatid, motid, sex,
affected )

Farrel Buchinsky, MD
Pediatric Otolaryngologist
Allegheny General Hospital
Pittsburgh, PA 


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