Hi Jim, the idea is to compare the snp chip data to SNP calls derived from sequencing data. For the same samples, I have both SNP chip and sequencing data. To estimate the sensitivity and specificity, I want to compare the SNP chip data to sequencing data. >From sequencing data, I have a pileup-format file in a BED format: Chromosome From To Reference Base SNP call I have no experience working with SNP chip data. All I have is the data that looks like SNPID Call SNP_A-8373748 BB SNP_A-2210818 AB SNP_A-4290346 BB SNP_A-2219708 AA There are many questions: 1. I need to know where the SNP ID is Chromosome and position. From this I can deduce from what base it is on genome. 2. Convert what BB,AB and AA mean. Thanks Adrian On Thu, Jul 8, 2010 at 4:41 PM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Adrian, > > On 7/8/2010 12:59 PM, Adrian Johnson wrote: >> >> Hi: >> >> >> I have a snp array 6 (affymetrix) data table that looks like the >> following: >> >> >> SNPID ? ? ? ? ? ? ? ? ? Call >> SNP_A-8373748 ? BB >> SNP_A-2210818 ? AB >> SNP_A-4290346 ? BB >> SNP_A-2219708 ? AA >> >> >> I want to be able to convert this data into a .BED file like format >> that will look like following: > > Well, doing what you want will be difficult, as I don't know how you are > going from genotype to 'Reference Base' and 'Call', nor do I really know > what you mean by either of those in this situation. Anyway, that's a YP, not > an MP (for you Boogie Nights fans out there ;-D). > > Here is I think what you need to know to get close to what you are trying to > do. > >> library(pd.genomewidesnp.6) >> con <- db(pd.genomewidesnp.6) > ## fake up some IDs >> ids <- dbGetQuery(con, "select man_fsetid from featureSet limit 20;") >> ids > ? ? ?man_fsetid > 1 ?SNP_A-2131660 > 2 ?SNP_A-1967418 > 3 ?SNP_A-1969580 > 4 ?SNP_A-4263484 > 5 ?SNP_A-1978185 > 6 ?SNP_A-4264431 > 7 ?SNP_A-1980898 > 8 ?SNP_A-1983139 > 9 ?SNP_A-4265735 > 10 SNP_A-1995832 > 11 SNP_A-1995893 > 12 SNP_A-1997689 > 13 SNP_A-1997709 > 14 SNP_A-1997896 > 15 SNP_A-1997922 > 16 SNP_A-2000230 > 17 SNP_A-2000332 > 18 SNP_A-2000337 > 19 SNP_A-2000342 > 20 SNP_A-4268173 > > ## now a simple SQL query > >> dbGetQuery(con, paste("select chrom, physical_pos, allele_a, allele_b from >> featureSet where man_fsetid in ('", paste(ids[,1], collapse="','"), "');", >> sep = "")) > ? chrom physical_pos allele_a allele_b > 1 ? ? ?1 ? ? ?2224111 ? ? ? ?A ? ? ? ?G > 2 ? ? ?1 ? ? ?2319424 ? ? ? ?A ? ? ? ?G > 3 ? ? ?1 ? ? ?2926730 ? ? ? ?C ? ? ? ?T > 4 ? ? ?1 ? ? ?3084986 ? ? ? ?C ? ? ? ?G > 5 ? ? ?1 ? ? ?3155127 ? ? ? ?A ? ? ? ?C > 6 ? ? ?1 ? ? ?3695086 ? ? ? ?C ? ? ? ?G > 7 ? ? ?1 ? ? ?3710825 ? ? ? ?A ? ? ? ?G > 8 ? ? ?1 ? ? ?3753024 ? ? ? ?A ? ? ? ?G > 9 ? ? ?1 ? ? ?3753427 ? ? ? ?A ? ? ? ?G > 10 ? ? 1 ? ? ?3756100 ? ? ? ?A ? ? ? ?G > 11 ? ? 1 ? ? ?3756146 ? ? ? ?A ? ? ? ?C > 12 ? ? 1 ? ? ?4240737 ? ? ? ?A ? ? ? ?G > 13 ? ? 1 ? ? ?4243294 ? ? ? ?C ? ? ? ?G > 14 ? ? 1 ? ? ?4243405 ? ? ? ?A ? ? ? ?C > 15 ? ? 1 ? ? ?4243441 ? ? ? ?C ? ? ? ?T > 16 ? ? 1 ? ? ?1145994 ? ? ? ?C ? ? ? ?T > 17 ? ? 1 ? ? ?2543484 ? ? ? ?C ? ? ? ?T > 18 ? ? 1 ? ? ?2941694 ? ? ? ?C ? ? ? ?T > 19 ? ? 1 ? ? ?3292731 ? ? ? ?C ? ? ? ?T > 20 ? ? 1 ? ? ?4276892 ? ? ? ?C ? ? ? ?T > > If you don't know any SQL, note that there are a mixture of " and ' in that > paste statement, as we want to end up with a query that looks like this: > > "select chrom, physical_pos, allele_a, allele_b from featureSet where > man_fsetid in > ('SNP_A-2131660','SNP_A-1967418','SNP_A-1969580','SNP_A-4263484','SN P_A-1978185','SNP_A-4264431','SNP_A-1980898','SNP_A-1983139','SNP_A-42 65735','SNP_A-1995832','SNP_A-1995893','SNP_A-1997689','SNP_A-1997709' ,'SNP_A-1997896','SNP_A-1997922','SNP_A-2000230','SNP_A-2000332','SNP_ A-2000337','SNP_A-2000342','SNP_A-4268173');" > > Best, > > Jim > > > >> >> Chromosome ? ? Position ? ? ? ?Reference Base ? ? ? Call >> chr19 ? ? ? ? ? ? ? ?2094894 ? ? ? ? ? ? A ? ? ? ? ? ? ? ? ? ? ? ?T >> chr19 ? ? ? ? ? ? ? ?2095300 ? ? ? ? ? ? G ? ? ? ? ? ? ? ? ? ? ? ?A >> >> >> Is it possible through bioconductor? ?Thanks for your time. >> >> -Adrian >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues >