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

Dear Steven > I looked at older versions of snapCGH, and > indeed version 1.1.0 had a function > summarizeClones() > which has indeed disappeared :( It is a piity - but I know there is a reluctance to implement these functions from a Stats perspective. E.g SeLists define large regions of interests. The worry is that exporting the clones within such a region somehow validates the segmented feature as being the final result. From a Biologists view, we need the clone names because they are a short cut to getting back into the genome and enabling us to validate any imbalances by FISH or qPCR. They also make comparisons across samples easier for the non-stats minded people (me). > 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. It took me 12 hr yesterday to export and transform the MA$M and MA$genes data frames from snapCGH and get them in to aCGH compliant objects. I've made notes and will write a recipe when I am happy that what I've done is ok. Needless to say, it took me 11 hr to spot the extra white space introduced during the conversion ... One problem at the moment - snapCGH handles dye-swap easily because of LiMMAs modelMatrix function --> any idea how to do the same with aCGH > > 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). I will see whether this offers a short cut. Thanks for yout input. I feel I am making progress. best wishes, Ian

> > > > 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). > This is the answer - thanks for leading me here!!! a<-nudSegmentation(SegInfo.Bio.merge) # load a with all segmented data b<-a$regions[[sample#]] # load b with clone region data from a chosen sample show(b[1:10,]) # first 10 segmented regions from chosen sample ... Columns 1 and 2 give index numbers (x,y) for the clone names in this output show(a$genes[x:y,]) lists the clones !! Just need to learn enough R to script this ... Thanks again, Ian > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >