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.
Do you know of another method that would read the data and then write the
resultant data to a dataframe?
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))))
--
Farrel Buchinsky
Mobile: (412) 779-1073
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