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2013 Jul 02
2
Recoding variables based on reference values in data frame
I'm new to R (previously used SAS primarily) and I have a genetics data frame consisting of genotypes for each of 300+ subjects (ID1, ID2, ID3, ...) at 3000+ genetic locations (SNP1, SNP2, SNP3...). A small subset of the data is shown below: SNP_ID SNP1 SNP2 SNP3 SNP4 Maj_Allele C G C A Min_Allele T A T G ID1 CC GG CT AA ID2 CC GG CC AA ID3 CC GG nc AA ID4 _ _ _ _ ID5 CC GG CC AA ID6 CC GG CC AA ID7 CC GG CT AA ID8 _ _ _ _ ID9 CT GG CC AG ID10 CC GG CC AA...