[R] Repeating tdt function on thousands of variables

[Farrel Buchinsky]

I am using dgc.genetics to perform TDT analysis on SNP data from a cohort of 
trios.

I now have a file with about 6008 variables. The first few variables related 
to the pedigree data such as the pedigree ID the person ID etc. Thereafter 
each variable is a specific locus or marker. The variables are named by a 
pattern such as "Genotype.nnnnn" with nnnnn corresponding to a number which 
is the name or id of the locus.

I am able to get the tdt to run by each locus. >tdt(Genotype.914186, PGWide, 
famid, pid, fatid, motid, sex, affected )

Clearly I cannot type each locus in one at a time. Instead I want to loop it 
but am not sure how to do it. I tried lapply but it did not really work.

The example in Dalgaard's book, >sapply( thuesen, mean, na. rm= T) seems to 
work with basic functions but not with something like tdt. So how does one 
tell R to calculate the tdt for each variable and output the result to a 
dataframe in which one of the columns is the locus ID.?

Since I have another table in which every locus ID is in one column and in 
another column I have its chromosome number and exact position on the 
chromosome I could always create a vector out of the locusIDs but still I 
would need to know how to pass it on to the tdt function in R.


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