Hello Bioconductor, I am having some difficulties using the "snpMatrix" package. I download the following file using: >chr1<-read.HapMap.data(" http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/latest_phaseII+III_ ncbi_b36/forward/non- redundant/genotypes_chr1_CEU_r27_nr.b36_fwd.txt.gz " Next, I would like to calculate the linkage disequilibrium between these snps. I then try to get the ld between these sample by typing >> ld.snp(chr1) and get the following error Error in ld.snp(chr1) : snps argument must be of class snp.matrix/X.snp.matrix This is confusing to me because the vignette tells me that read.HapMap.data will download and convert the genotype data into a snp.matrix class object Any help is greatly appreciated. Thanks, Pete [[alternative HTML version deleted]]

On Thu, Jun 30, 2011 at 2:04 AM, rna seq <rna.seeker@gmail.com> wrote: > Hello Bioconductor, > > I am having some difficulties using the "snpMatrix" package. I download the > following file using: > > >chr1<-read.HapMap.data(" > > http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/latest_phaseII+II I_ncbi_b36/forward/non- redundant/genotypes_chr1_CEU_r27_nr.b36_fwd.txt.gz > " > > Next, I would like to calculate the linkage disequilibrium between these > snps. I then try to get the ld between these sample by typing > > >> ld.snp(chr1) > > and get the following error > Error in ld.snp(chr1) : > snps argument must be of class snp.matrix/X.snp.matrix > > read.HapMap.data returns a list that includes a snp.matrix and some metadata support. i believe that ld.snp(chr1[[1]]) would work use class(chr1), str(chr1) and str(chr1[[1]]) and so forth to diagnose such situations, and read the man page for read.* to understand fully the returned object also please supply sessionInfo() result for all queries. > This is confusing to me because the vignette tells me that read.HapMap.data > will download and convert the genotype data into a snp.matrix class object > > Any help is greatly appreciated. > > Thanks, > > Pete > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

read.HapMap.data() does not return an object of class "snp.matrix". It returns a list whose first element is the snp.matrix object. See the online help page On 30/06/11 01:04, rna seq wrote: > Hello Bioconductor, > > I am having some difficulties using the "snpMatrix" package. I download the > following file using: > >> chr1<-read.HapMap.data(" > http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/latest_phaseII+II I_ncbi_b36/forward/non- redundant/genotypes_chr1_CEU_r27_nr.b36_fwd.txt.gz > " > > Next, I would like to calculate the linkage disequilibrium between these > snps. I then try to get the ld between these sample by typing > >>> ld.snp(chr1) > > and get the following error > Error in ld.snp(chr1) : > snps argument must be of class snp.matrix/X.snp.matrix > > This is confusing to me because the vignette tells me that read.HapMap.data > will download and convert the genotype data into a snp.matrix class object > > Any help is greatly appreciated. > > Thanks, > > Pete > > [[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 -- Professor David Clayton Wellcome Trust/Juvenile Diabetes Research Foundation Principal Research Fellow Diabetes and Inflammation Laboratory Cambridge University, Department of Medical Genetics Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY Tel: (44) 1223 762669 Email: david.clayton at cimr.cam.ac.uk