[R] Repeating tdt function on thousands of variables

Uwe Ligges ligges at statistik.uni-dortmund.de
Wed May 3 08:41:30 CEST 2006

Farrel Buchinsky wrote:

> 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 )

Looks like you have to be much more specific:

R> tdt(Genotype.914186, PGWide, famid, pid, fatid, motid, sex, affected)
Error: could not find function "tdt"

Uwe Ligges

> 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.

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