> If I run an analysis which generates statistical tests on many SNPs I would > naturally want to get more details on the most significant SNPs. Directly > from within R one can get the information by loading RSNPer (from > Bioconductor) and simply issuing a command SNPinfo(2073285). Unfortunately, > the command cannot handle a vector and therefore only wants to do one at a > time. > I tried the lapply and sapply functions but was stymied temporarily > lapply(best.snp,SNPinfo) #where best.snp is a vector of SNPs > Error in FREQ[[1]] : subscript out of bounds [I do not know what that means] > Nevertheless, I found that one of the SNPs was causing this and could bypass > it by using the try function. > > lapply(best.snp,function(x) try(SNPinfo(x))) which let R continue > One can then extract numbers or values out of the resultant output but this > method lacks finesse and is not easy.
looks pretty easy to me. there is the nuisance of digging through the output but i have no use cases or -- to my knowledge, until you wrote -- any active users other than myself. so little motivation to push further. additionally, snpper is not particularly well maintained (builds seem pretty old) and i think it is going to be replaced. so i don't plan to put much more effort into it until i learn more about snpper.chip.org durability. > > Do you know of another method that would read the data and then write the > resultant data to a dataframe? i think you'll be able to do this with your lapply -- and contribute the code? > > Another very useful feature for which I would like to use the same treatment > is to use the SNPinfo as a way to get the gene information > lapply(best.snp,function(x) try(geneDetails(SNPinfo(x)))) as above ______________________________________________ [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 and provide commented, minimal, self-contained, reproducible code.
