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"?
2) Is there a way to run segmentation on single, or a subset of
profiles in a "AromaUnitTotalCnBinarySet"?
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"?
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.
Best,
Kai
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