Hi Ian, On 25 Jun 2007, at 11:58, Ian Roberts wrote: > > > I've got snapCGH set up and running well - and drawing all the > plots I need. However I am struggling to export a list of clones > from the summarize.clones function. That is, a list of clones > present in the segmented regions of the genome across all samples > contained in the SegInfo object. I am sure a function was > available in earlier snapCGH versions 'export clones' but doesn't > seem to be there now? > > Thanks for your help. > > > > Ian > > > > __________________ > Ian Roberts PhD > MRC Cancer Cell Unit > Hutchison/MRC Research Centre > Box 197 > Hills Road > Cambridge. CB2 0XZ > United Kingdom > > Tel +44 1223 763 279 > > ir210 at hutchison-mrc.cam.ac.uk > www.hutchison-mrc.cam.ac.uk > > > Using the latest version of snapCGH() installed with biocLite(), I see that the current version of the function summarize.clones() returns a data frame of results. (Note also that summarize.clones() is in the package "aCGH" that snapCGH loads.) The return clause of the function is wrapped with "invisible()" so you won't see the returned data frame if you invoke the command in an interactive R session. The help page for summarize.clones() shows a basic example data(colorectal) summarize.clones(colorectal) You can capture the resultant data frame into a user variable, e.g. foo <- summarize.clones(colorectal) Object "foo" will be a data frame that you can view, or export to an external file using write.table() or write.csv(). Or you can just output the results of summarize.clones() directly, e.g. write.csv(summarize.clones(colorectal), file = "colo.clone.summary.csv") Hope this answers your question. Steven McKinney More details: > sessionInfo() R version 2.5.0 (2007-04-23) powerpc-apple-darwin8.9.1 locale: en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] "splines" "grid" "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: snapCGH aCGH sma multtest cluster GLAD aws DNAcopy tilingArray pixmap "1.4.0" "1.10.0" "0.5.15" "1.14.0" "1.11.6" "1.10.0" "1.3-2" "1.10.0" "1.14.0" "0.4-7" geneplotter annotate genefilter survival vsn strucchange sandwich zoo RColorBrewer affy "1.14.0" "1.14.1" "1.14.1" "2.31" "2.2.0" "1.3-2" "2.0-2" "1.3-1" "0.2-3" "1.14.0" affyio Biobase limma glmmADMB lattice DBI RODBC "1.4.0" "1.14.0" "2.10.4" "0.3" "0.15-5" "0.2-3" "1.2-1" > summarize.clones(colorectal) > foo <- summarize.clones(colorectal) > class(foo) [1] "data.frame" > dim(foo) [1] 2031 10 > foo[1:10, ] Clone Target Chrom kb NumPresent.All NumGain.All NumLost.All PropPresent.All PropGain.All PropLost.All 2 RP11-82D16 HumArray2H11_C9 1 2009 39 4 7 0.98 0.10 0.18 3 RP11-62M23 HumArray2H10_N30 1 3368 35 1 7 0.88 0.03 0.20 4 RP11-111O5 HumArray2H10_B18 1 4262 38 1 9 0.95 0.03 0.24 5 RP11-51B4 HumArray2H10_Q30 1 6069 35 0 10 0.88 0.00 0.29 6 RP11-60J11 HumArray2H10_T30 1 6817 36 1 7 0.90 0.03 0.19 7 RP11-813J5 HumArray2H10_B19 1 9498 30 0 8 0.75 0.00 0.27 8 RP11-199O1 HumArray2H10_W30 1 10284 39 1 5 0.98 0.03 0.13 9 RP11-188F7 HumArray2H9_C14 1 12042 36 1 4 0.90 0.03 0.11 10 RP11-178M15 HumArray2H9_F14 1 13349 35 1 4 0.88 0.03 0.11 11 RP11-219F4 HumArray2H9_I14 1 14391 39 1 7 0.98 0.03 0.18 > attributes(foo) $names [1] "Clone" "Target" "Chrom" "kb" "NumPresent.All" "NumGain.All" "NumLost.All" [8] "PropPresent.All" "PropGain.All" "PropLost.All" $row.names [1] "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" ..... > write.csv(summarize.clones(colorectal), file = "colo.clone.summary.csv") > summarize.clones function (aCGH.obj, resT = NULL, pheno = rep(1, ncol(aCGH.obj)), rsp.uniq = unique(pheno), thres = 0.25, factor = 2.5, all = length(rsp.uniq) == 1 && is.null(resT), titles = if (all) "all" else rsp.uniq) { if (!is.null(sd.samples(aCGH.obj)) && (factor > 0)) { thres <- factor * (sd.samples(aCGH.obj)$madGenome) } data <- log2.ratios(aCGH.obj) datainfo <- clones.info(aCGH.obj) rsp.uniq <- sort(rsp.uniq) colmatr <- if (length(rsp.uniq) > 1) t(sapply(rsp.uniq, function(rsp.uniq.level) ifelse(pheno == rsp.uniq.level, 1, 0))) else matrix(rep(1, length(pheno)), ncol = length(pheno), nrow = 1) data.thres <- threshold.func(data, posThres = thres) bac.summary <- table.bac.func(dat = data.thres, colMatr = colmatr) if (!is.null(resT)) { res <- resT[order(resT$index), ] bac.summary <- cbind(bac.summary, res$teststat, res$rawp, res$adjp) } bac.summary <- as.data.frame(bac.summary) nms <- c("NumPresent", "NumGain", "NumLost", "PropPresent", "PropGain", "PropLost") cnames <- colnames(bac.summary) cnames[1:6] <- paste(nms, "All", sep = ".") if (nrow(colmatr) > 1) for (m in 1:length(rsp.uniq)) cnames[(6 * m + 1):(6 * (m + 1))] <- paste(nms, titles[m], sep = ".") if (!is.null(resT)) cnames[(ncol(bac.summary) - 2):ncol(bac.summary)] <- c("stat", "rawp", "adjp") colnames(bac.summary) <- cnames bac.summary <- cbind(datainfo, bac.summary) invisible(bac.summary) } Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney at bccrc.ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -----Original Message----- From: Natalie Thorne [mailto:npt22@cam.ac.uk] Sent: Mon 6/25/2007 5:15 AM To: ir210 at hutchison-mrc.cam.ac.uk Cc: Mike Smith; J-C. Marioni; Steven McKinney Subject: Re: snapCGH Hi Ian, I've no idea about this specific question as I'm not the maintainer of snapCGH. Mike Smith would know about this since he wrote most of the code - I don't know if he has finished his exams yet or not. Steve McKinney might also be able to help. I've cc'd Mike and Steve to see if they can answer your question. They will probably forward the question and response to the Bioconductor mail list, since this is the forum that is usually used for asking and answering any questions about bioc packages (i.e. others may have similar questions or find the answers and discussions useful). You'll probably find emailing the bioc list the fastest way to get a (useful) response in the future. Natalie On 25 Jun 2007, at 11:58, Ian Roberts wrote: > Dear Nathalie, > > > > Hope you are well, and don't mind an email question about snapCGH - > I asked John, but haven't heard back so assume he is off writing > thesis. > > > > I've got snapCGH set up and running well - and drawing all the > plots I need. However I am struggling to export a list of clones > from the summarize.clones function. That is, a list of clones > present in the segmented regions of the genome across all samples > contained in the SegInfo object. I am sure a function was > available in earlier snapCGH versions 'export clones' but doesn't > seem to be there now? > > Thanks for your help. > > > > Ian > > > > __________________ > Ian Roberts PhD > MRC Cancer Cell Unit > Hutchison/MRC Research Centre > Box 197 > Hills Road > Cambridge. CB2 0XZ > United Kingdom > > Tel +44 1223 763 279 > > ir210 at hutchison-mrc.cam.ac.uk > www.hutchison-mrc.cam.ac.uk > > >

Hi Ian, I looked at older versions of snapCGH, and indeed version 1.1.0 had a function summarizeClones() which has indeed disappeared :( I do not see a straightforward way of converting a SegList object to an aCGH type object, I'm not up to date on the definitions of the various components of snapCGH's SegList and aCGH objects. For example, summarize.clones() seems to work with kb units for clone positions but snapCGH works with Mb units so some care is needed to convert objects. Output for snapCGH at present appears to be all graphical. The function nudSegmentation() in snapCGH appears to generate the type of data from which output similar to that from summarize.clones() could be obtained (see the "regions" component of nudSegmentation output). Mike and John - do you have any plans to implement a function like the old summarizeClones() function to produce output similar to summarize.clones() for SegList objects? Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney at bccrc.ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Ian Roberts Sent: Tue 6/26/2007 12:52 AM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC]snapCGH; export results of summarize.clones() function from aCGH Steven McKinney <smckinney at="" ...=""> writes: > > Hi Ian, > > On 25 Jun 2007, at 11:58, Ian Roberts wrote: > > > > > > > I've got snapCGH set up and running well - and drawing all the > > plots I need. However I am struggling to export a list of clones > > from the summarize.clones function. That is, a list of clones > > present in the segmented regions of the genome across all samples > > contained in the SegInfo object. I am sure a function was > > available in earlier snapCGH versions 'export clones' but doesn't > > seem to be there now? > > > > Thanks for your help. > > > > > > > > Ian > > Using the latest version of snapCGH() installed with > biocLite(), I see that the current version of the > function summarize.clones() returns a data frame > of results. > > (Note also that summarize.clones() is in the > package "aCGH" that snapCGH loads.) > > The return clause of the function > is wrapped with "invisible()" so you won't > see the returned data frame if you invoke the > command in an interactive R session. > > The help page for summarize.clones() shows > a basic example > > data(colorectal) > summarize.clones(colorectal) > > You can capture the resultant > data frame into a user variable, e.g. > > foo <- summarize.clones(colorectal) > > Object "foo" will be a data frame that > you can view, or export to an external > file using write.table() or write.csv(). > > Or you can just output the results of > summarize.clones() directly, e.g. > > write.csv(summarize.clones(colorectal), file = "colo.clone.summary.csv") > > Dear Steven, Thanks very much for your reply. Unfortunately being an R newbie, and still relatively unfamiliar with snapCGH and aCGG packatges I've been unable to get your suggestion working. Effectively, snapCGH ends up with a SegList (e.g. SegInfo.Bio.merge) that contains the required information. SegList is An object of class "SegList" I see that summarize.clones is an aCGH function that takes aCGH.objects as targets. Consequently if I do: > results<-summarize.clones(SegInfo.Bio.merge) I get ... Error in rep(posThres, ncol(dat)) : invalid 'times' argument ... and I have no idea what that means. I suspect there is some easy method to convert SegLists to aCGH objects, and would appreciate any help available in that regard. Thanks for your assistance. Best wishes, Ian _______________________________________________ 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