Thank you very much, Henrik. What you suggested is working very well.
Best,
Kai
On Dec 2, 10:18 pm, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> Hi.
>
> On Thu, Dec 2, 2010 at 10:24 AM, Kai <wangz...@gmail.com> wrote:
> > Hi Henrik,
>
> > I was trying to run segmentation on a large set of ~300 SNP genotyping
> > array profiles. Currently I am loading all the profiles into aroma and
> > run the segmenter on them one by one, which takes a really long time.
> > I was wondering whether there is a way to break the computation into
> > parts and run all the parts simultaneously. Specifically:
>
> > 1) Is there a way to load only a subset of profiles in a project into
> > a "AromaUnitTotalCnBinarySet"?
>
> It is true that ds <- AromaUnitTotalCnBinarySet$byName(...) will setup
> a set containing all data files. However, after that you can always
> subset using extract(), e.g. ds <- extract(ds, 1:5);
>
> > 2) Is there a way to run segmentation on single, or a subset of
> > profiles in a "AromaUnitTotalCnBinarySet"?
>
> Yes, either by subsetting as above already from start or simply by
> specifying the 'arrays' argument to fit()/process() [below]. Note
> that the latter is a more convenient approach for various reasons.
> First, if the reference used to calculate CN ratios is the robust
> average across all samples, then you do not have to worry about
> getting it correct. (This is not a problem in your particular case
> because you use that cbs$.calculateRatios <- FALSE feature). Second,
> the final ChromosomeExplorer HTML page correctly list all samples. If
> you subset immediately after setting up the data set (as above), then
> you basically have to make sure to process() one ChromosomeExplorer on
> all arrays.
>
> > 3) Assuming that one can generate the CBS segmentation model on single
> > profiles, is there a way to load them together back in to aroma and
> > pass to the "ChromosomeExplorer"?
>
> Yes. The simplest way is to simply run what you are doing below ones
> at the very end. Already segmented and process samples will be
> skipped, also already generated image files etc.
>
>
>
>
>
> > The current process I have (which performs segmentation one sample at
> > a time) is implemented as follows:
>
> > # segment by CBS model
> > ds = AromaUnitTotalCnBinarySet
> > $byName("dataset,paired",chipType="HumanOmni1-Quad");
>
> > cbs = CbsModel(ds);
> > cbs$.calculateRatios = FALSE;
>
> > fit(cbs, chromosomes=c(1:23), min.width=5, undo.splits="sdundo",
> > undo.SD=1, verbose=2);
>
> > # display data and segmentation in ChromosomeExplorer
> > ce = ChromosomeExplorer(cbs);
> > process(ce,chromosomes=c(1:23));
>
> > Any other suggestion you may provide is also highly appreciated. Thank
> > you very much.
>
> library("aroma.core");
> verbose <- Arguments$getVerbose(-4, timestamp=TRUE);
>
> # Arrays that your host should process
> arrays <- 5:8; # Change for different hosts
>
> # Setup the complete data set
> ds <-
> AromaUnitTotalCnBinarySet$byName("dataset,paired",chipType="HumanOmni1-Quad");
>
> # Setup the "complete" segmentation model
> cbs <- CbsModel(ds, min.width=5, undo.splits="sdundo", undo.SD=1);
> cbs$.calculateRatios <- FALSE;
>
> # Fit a subset of the arrays
> fit(cbs, arrays=arrays, chromosomes=c(1:23), verbose=verbose);
>
> # Setup the "complete" ChromosomeExplorer, ...
> ce <- ChromosomeExplorer(cbs);
>
> # ...but generate PNG image files only for a subset
> process(ce, arrays=arrays, chromosomes=c(1:23), verbose=verbose);
>
> Note that you actually do not have to call fit() explicitly, because
> process() will do it implicitly (with the same arguments).
>
> If you want to call the above script from the command line, then
> replace the arrays <- ... line with
>
> arrays <- commandArgs(asValue=TRUE)$arrays;
> arrays <- eval(parse(text=arrays));
> arrays <- Arguments$getIndices(arrays);
>
> and then you can run the above by:
>
> R --args --arrays=1:5 < script.R
>
> Hope this helps
>
> Henrik
>
>
>
> > Best,
> > Kai
>
> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> > version of the package, 2) to report the output of sessionInfo() and
> > traceback(), and 3) to post a complete code example.
>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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