Hello, Currently I am trying to load chr1 into a snp.matrix and from this matrix, I am tring to calculate the "ld" between two snps, when I enter >pair.result.ld.snp(chr1[[1]], 748682, 748704) I get the following errors. Any clues here would help. SESSION_ Information: samples = 174, snps = 314024 ii = 748682, jj = 748704 *** caught segfault *** address 0xb7f9153e, cause 'memory not mapped' Traceback: 1: .Call("snp_pairwise", snpdata, loc.snpA, loc.snpB, PACKAGE = "snpMatrix") 2: pair.result.ld.snp(chr1[[1]], 748682, 748704) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: 1 aborting ... Segmentation fault > sessionInfo() R version 2.12.1 (2010-12-16) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] snpMatrix_1.14.6 survival_2.36-5 s On Wed, Jun 29, 2011 at 10:31 PM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > > > 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+I II_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]]