On Tue, Nov 29, 2011 at 5:20 AM, francy [guest] wrote: > > Hi all, > > I am trying to find eQTLs in or around a particular gene with probe ID= > "10023813203" (gene is APOE). I have first selected the SNPs on only my > chromosome of interest (chr19), then imported the plink files only for this > chromosome doing this: > > snp.matrix<-read.plink("plink.bed", "plink.bim", > "plink.fam",select.snps=chr19) > > I was able to create an expression set (called 'es'), and a sml_Set by > doing this: > > ss<- make_smlSet(es, list("1"=snp.matrix$genotypes)) > > but I can't seem to go beyond and use this sml_Set to perform the > association. > > When I try this or other combinations of this (e.g. using 'APOE') > f1 = gwSnpTests(probeId("10023813203"), ss) > > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "gwSnpTests", for > signature "character", "smlSet", "missing", "missing" > > When you encounter an error of this sort, please check what signatures are supported: > showMethods("gwSnpTests") Function: gwSnpTests (package GGtools) sym="formula", sms="smlSet", cnum="cnumOrMissing", cs="missing" sym="formula", sms="smlSet", cnum="snpdepth", cs="missing" This shows that the first argument should be a formula, and suggests that you can have only two arguments if you like. If you change your call to f1 = gwSnpTests(probeId("10023813203")~1, ss) I would expect it to succeed. Note the example code, from R 2.14, which you really should be using at this time: > hmceuB36.2021 <- getSS("GGtools", c("20", "21")) # construct smlSet from prepackaged data > hmFou = hmceuB36.2021[, which(hmceuB36.2021$isFounder)] # filter samples to 'founders' > f1 = gwSnpTests(genesym("CPNE1")~male, hmFou, chrnum(20)) # execute simple set of tests > f1 # there are 119921 tests, so have a concise report gwSnpScreenResult for gene CPNE1 [probe GI_23397697-A ] > topSnps(f1) # get top results p.val rs17093026 3.735759e-10 rs1118233 1.272958e-09 rs12480408 1.360682e-09 rs6060535 1.360682e-09 rs11696527 1.360682e-09 rs6058303 1.360682e-09 rs6060578 1.360682e-09 rs2425078 1.360682e-09 rs1970357 1.360682e-09 rs7273815 1.806197e-09 > My first question is, why is the 'gwSnpTests' not working? > Please use a supported call sequence. > My second question is, do I have to select the chromosome I am interested > in before creating the sml test? I would have liked to select chromosome 19 > after so that I could analyse more than this one chromosome if I wanted > to…Is this possible?? It seems as the snp.matrix must be in the form of a > list, so maybe I have to create a list of all the chromosomes? > THANK YOU VERY VERY MUCH FOR ANY HELP YOU COULD GIVE ME!! I really > appreciate it! > > The signatures show that you can omit the chromosome if you wish. In this case, > f2 = gwSnpTests(genesym("CPNE1")~male, hmFou) > f2 gwSnpScreenResult for gene CPNE1 [probe GI_23397697-A ] > topSnps(f2) $`20` p.val rs17093026 3.735759e-10 rs1118233 1.272958e-09 rs12480408 1.360682e-09 rs6060535 1.360682e-09 rs11696527 1.360682e-09 rs6058303 1.360682e-09 rs6060578 1.360682e-09 rs2425078 1.360682e-09 rs1970357 1.360682e-09 rs7273815 1.806197e-09 $`21` p.val rs2823672 3.024310e-05 rs4257464 4.340207e-05 rs16994832 4.340207e-05 rs2823676 4.340207e-05 rs2823677 4.340207e-05 rs8131686 4.340207e-05 rs2823683 4.340207e-05 rs238983 4.340207e-05 rs2828436 4.340207e-05 rs2828438 4.340207e-05 gwSnpTests will operate on all the SNPs in the smList(smlSet) and return lists organized by chromosome. Hence the "gw" -- it is possible to compute a genome-wide search for eQTL if the smlSet contains SNP from all chromosomes. A few years ago this was quite reasonable when we handled, say, 4 million SNP. Then it became less reasonable when we started to work with 8 million SNP. So the infrastructure changed to deemphasize working with all chromosomes at once -- thus the introduction of getSS() to construct the smlSet for a selected set (typically only one) of chromosomes of SNP. Concisely computing and managing results from transcriptome x genome searches is addressed by the eqtlTests function and by genewiseFDRtab ... these functions are under development to simplify these tasks, which can be arduous as large imputed SNP panels come into play. Thus it is relevant to work with the devel branch as you start hitting limits. I will provide more news as work proceeds. As the initial discussion of this topic occurred on biostar list, I will note for other readers that a tutorial on using GGtools with R 2.14 is available at ismb11gg.wordpress.com, and that the ggtut experimental data package underlies the tutorial. Of note is that ggtut will not pass check with R devel, because some serialized objects conflict with revised class definitions. This will be sorted before too long. > -- output of sessionInfo(): > I strongly advise you to upgrade to R 2.14. My sessionInfo for the runs above is R version 2.14.0 Patched (2011-11-09 r57622) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591 [5] LC_MONETARY=en_US.iso88591 LC_MESSAGES=en_US.iso88591 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices datasets tools utils [8] methods base other attached packages: [1] illuminaHumanv1.db_1.12.1 GGtools_4.1.8 [3] ff_2.2-3 bit_1.1-7 [5] GenomicRanges_1.6.2 org.Hs.eg.db_2.6.4 [7] rtracklayer_1.14.2 RCurl_1.7-0 [9] bitops_1.0-4.1 IRanges_1.12.1 [11] annotate_1.32.0 AnnotationDbi_1.16.2 [13] GGBase_3.15.2 genefilter_1.36.0 [15] RSQLite_0.10.0 DBI_0.2-5 [17] snpStats_1.4.0 Matrix_1.0-1 [19] lattice_0.20-0 survival_2.36-10 [21] BiocGenerics_0.1.0 Biobase_2.14.0 [23] weaver_1.20.0 codetools_0.2-8 [25] digest_0.5.1 BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] Biostrings_2.22.0 BSgenome_1.22.0 grid_2.14.0 Rsamtools_1.7.1 [5] XML_3.4-3 xtable_1.6-0 zlibbioc_1.0.0 > > > sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] tools splines stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] GGtools_3.10.2 ff_2.2-3 bit_1.1-7 > [4] GenomicRanges_1.4.8 org.Hs.eg.db_2.5.0 rtracklayer_1.12.5 > [7] RCurl_1.6-10 bitops_1.0-4.1 IRanges_1.10.6 > [10] annotate_1.30.1 AnnotationDbi_1.14.1 GGBase_3.12.0 > [13] RSQLite_0.10.0 DBI_0.2-5 snpStats_1.2.1 > [16] Matrix_0.999375-50 lattice_0.19-33 survival_2.36-9 > [19] Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] Biostrings_2.20.4 BSgenome_1.20.1 grid_2.13.1 XML_3.4-3 > [5] xtable_1.5-6 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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]]