Hello I have used as.geneSet in the GeneticsBase package to deal with some SNP data, and i want to make sure that the package handles it they way i want it to. So i want to make sure that the programe genotypes the alleles correct, and by that i mean making a table like this guy did (he did it with the same data as mine, but he had more data). > y gentype genotype [1,] "0_A2M_DS066406.1_15" "AG" "2" [2,] "0_A2M_DS066406.1_15" "GG" "3" [3,] "0_A2M_DS068238.1_4" "AG" "2" [4,] "0_A2M_DS068238.1_4" "GG" "3" [5,] "0_A2M_DS068238.1_4" "AA" "1" [6,] "0_ABCA1_DS062937.1_32" "AG" "2" [7,] "0_ABCA1_DS062937.1_32" "GG" "3" [8,] "0_ABCA1_DS062937.1_32" "AA" "1" [9,] "0_ABCA1_DS073864.1_41" "AG" "2" [10,] "0_ABCA1_DS073864.1_41" "GG" "3" [11,] "0_ABCA1_DS073864.1_41" "AA" "1" [12,] "0_ABCA1_DS073864.1_41_2" "AG" "2" [13,] "0_ABCA1_DS073864.1_41_2" "GG" "3" [14,] "0_ABCA1_DS073864.1_41_2" "AA" "1" [15,] "0_ABCA1_DS078984.1_39" "AT" "2" [16,] "0_ABCA1_DS078984.1_39" "TT" "3" [17,] "0_ABCA1_DS078984.1_39" "AA" "1" [18,] "0_ABCA1_DS082793.1_19" "AG" "2" [19,] "0_ABCA1_DS082793.1_19" "GG" "3" [20,] "0_ABCA1_DS082793.1_19" "AA" "1" [21,] "0_ABCC10_DS066718.1_3" "AC" "2" [22,] "0_ABCC10_DS066718.1_3" "CC" "3" [23,] "0_ABCC6_DS063353.1_20" "AC" "2" [24,] "0_ABCC6_DS063353.1_20" "CC" "3" [25,] "0_ABCC6_DS063353.1_20" "AA" "1" [26,] "0_AARSL_DS061819.1_2" "GG" "1" Im pretty sure that GeneticsBase handle it the right way, cause i can se that using alleleCount() and alleleLevels(). I already have the table with the SNP-ID, and with the allele combination: > z <- cbind(unlist(genotypeLevels(gs))) > z [,1] X0_A2M_DS066406.1_151 "G/G" X0_A2M_DS066406.1_152 "G/A" X0_A2M_DS068238.1_41 "G/G" X0_A2M_DS068238.1_42 "G/A" X0_A2M_DS068238.1_43 "A/A" X0_ABCA1_DS062937.1_321 "G/G" X0_ABCA1_DS062937.1_322 "G/A" X0_ABCA1_DS062937.1_323 "A/A" X0_ABCA1_DS062937.1_324 "NA/NA" X0_ABCA1_DS073864.1_411 "G/G" X0_ABCA1_DS073864.1_412 "G/A" X0_ABCA1_DS073864.1_413 "A/A" X0_ABCA1_DS073864.1_414 "NA/NA" X0_ABCA1_DS073864.1_41_21 "A/A" X0_ABCA1_DS073864.1_41_22 "A/G" X0_ABCA1_DS073864.1_41_23 "G/G" X0_ABCA1_DS073864.1_41_24 "NA/NA" X0_ABCA1_DS078984.1_391 "A/A" X0_ABCA1_DS078984.1_392 "A/T" X0_ABCA1_DS078984.1_393 "T/T" X0_ABCA1_DS078984.1_394 "NA/NA" X0_ABCA1_DS082793.1_191 "G/G" X0_ABCA1_DS082793.1_192 "G/A" X0_ABCA1_DS082793.1_193 "A/A" X0_ABCC10_DS066718.1_31 "C/C" X0_ABCC10_DS066718.1_32 "NA/NA" X0_ABCC10_DS066718.1_33 "C/A" X0_ABCC6_DS063353.1_201 "A/C" X0_ABCC6_DS063353.1_202 "A/A" X0_ABCC6_DS063353.1_203 "C/C" X0_ABCC6_DS063353.1_204 "NA/NA" X0_AARSL_DS061819.1_21 "G/G" X0_AARSL_DS061819.1_22 "NA/NA" So what I miss is the column with the genotypes (like the other guy), which i get from allelCount(). Can anyone help me with that. Regards, Johannes > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=Danish_Denmark.1252;LC_CTYPE=Danish_Denmark.1252;LC_MONETAR Y=Danish_Denmark.1252;LC_NUMERIC=C;LC_TIME=Danish_Denmark.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GeneticsBase_1.8.0 haplo.stats_1.3.8 mvtnorm_0.9-5 xtable_1.5-4 combinat_0.0-6 loaded via a namespace (and not attached): [1] gdata_2.4.2 gplots_2.6.0 gtools_2.5.0 MASS_7.2-44 tools_2.8.0