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 ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
