Hi, I am trying to upload SNP data to SNPassoc package for basic HWE check and analysis of association between snp and a trait. In my file the genotypes are coded 0, 1, 2. I have problem in uploading it to SNPassoc package as the setupSNP function does not seem to accept the file without sep="" option. I would be very grateful for your help. I paste below my code. > SNPs <- read.delim("H:/genetics_data.txt") > SNPs[1:10,270:275] phenotype snp4912075_c snp9426794_c snp6673711_c snp11506_g snp12065621_g 1 2 0 0 0 2 0 2 1 0 0 0 0 0 3 1 1 0 1 0 0 4 1 2 0 1 0 2 5 1 1 0 1 0 1 6 1 1 0 1 0 1 7 1 0 0 0 0 1 8 1 1 0 1 0 0 9 1 1 0 1 0 0 10 1 1 0 1 1 0 > myData<-setupSNP(data=SNPs, colSNPs=271:534) Error in FUN(X[[1L]], ...) : choose the correct character separator to divide alleles Thank you very much. Kind regards, Magdalena > sessionInfo()R version 2.15.2 (2012-10-26) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] SNPassoc_1.8-5 survival_2.37-2 haplo.stats_1.6.3 genetics_1.3.8 mvtnorm_0.9-9994 [6] MASS_7.3-23 gtools_2.7.0 gdata_2.12.0 combinat_0.0-8 loaded via a namespace (and not attached): [1] tools_2.15.2 [[alternative HTML version deleted]]

Hi Magdalena, SNPassoc is not a Bioconductor package. You could try posting your question to R-help at http://www.r-project.org/mail.html. A couple of Bioconductor packages that may fit your need are snpStats, FunciSNP and GWAStools. Valerie On 02/25/2013 07:24 AM, Magdalena Wozniak wrote: > Hi, > I am trying to upload SNP data to SNPassoc package for basic HWE check and > analysis of association between snp and a trait. In my file the genotypes > are coded 0, 1, 2. I have problem in uploading it to SNPassoc package as > the setupSNP function does not seem to accept the file without sep="" > option. I would be very grateful for your help. > I paste below my code. > >> SNPs <- read.delim("H:/genetics_data.txt") > >> SNPs[1:10,270:275] > > phenotype snp4912075_c snp9426794_c snp6673711_c snp11506_g snp12065621_g > > 1 2 0 0 0 2 0 > > 2 1 0 0 0 0 0 > > 3 1 1 0 1 0 0 > > 4 1 2 0 1 0 2 > > 5 1 1 0 1 0 1 > > 6 1 1 0 1 0 1 > > 7 1 0 0 0 0 1 > > 8 1 1 0 1 0 0 > > 9 1 1 0 1 0 0 > > 10 1 1 0 1 1 0 > >> myData<-setupSNP(data=SNPs, colSNPs=271:534) > > Error in FUN(X[[1L]], ...) : > > choose the correct character separator to divide alleles > > > > Thank you very much. > > Kind regards, > > Magdalena > > >> sessionInfo()R version 2.15.2 (2012-10-26) > Platform: i386-w64-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] splines stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] SNPassoc_1.8-5 survival_2.37-2 haplo.stats_1.6.3 > genetics_1.3.8 mvtnorm_0.9-9994 > [6] MASS_7.3-23 gtools_2.7.0 gdata_2.12.0 combinat_0.0-8 > > loaded via a namespace (and not attached): > [1] tools_2.15.2 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >