User: Günter Klambauer

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370
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Austria
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http://www.bioinf.jku....
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Posts by Günter Klambauer

<prev • 63 results • page 1 of 7 • next >
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Answer: A: cn.mops encounter negative width problem
... Hello, Great that you figured out the problem with your BED file! About your second question: "CN2" is the symbol cn.MOPS uses for the normal state (non-CNV state). If you check the slot "cnvr(result)", then you will see a lot of "CN2", because a CNV region in the genome is displayed, in which at ...
written 29 days ago by Günter Klambauer370
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Answer: A: R code for cn.mops -- if a chromosome does not have CNV ?
... Hello again, And apologies, again, I had not seen your message until now. I see that the error is problematic for your pipeline  - you can try to catch the error using "try()". However, I will change the behaviour from "error" to "warning" in the next version of cn.mops. You don't need to change y ...
written 4 weeks ago by Günter Klambauer370
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Answer: A: R code for cn.mops
... Hello Bogdan, Apologies - I had overseen your questions. I hope you still had success with cn.mops - thanks for using it.   The code seems ok to me! If you have a validation set with known CNVs, you should adjust the parameters, like normalization, window length, etc, to optimize the performance ...
written 4 weeks ago by Günter Klambauer370
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Answer: A: cn.mops encounter negative width problem
... Hello again, This error occurs if there is some inconsistency in the BED file (the one that defines the segments in which the reads are counted) that you use to run "getSegmentReadCountsFromBAM" (I assume you used that function, right?). Please check, if your BED file is correct, i.e. segment ends ...
written 4 weeks ago by Günter Klambauer370
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Answer: A: which cn.mops function should I use
... referencecn.mops is the correct choice for your setting! The parameters of "exomecn.mops" are adjusted to a non-tumor copy number setting. ...
written 4 weeks ago by Günter Klambauer370
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Answer: A: cn.mops returning only "NA" as copy number
... This is the default behaviour. The function "calcIntegerCopyNumbers" replaces the NA values with integer copy numbers. Regards, Günter On 2017-03-11 00:15, rc16955 [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> ...
written 10 weeks ago by Günter Klambauer370
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Comment: C: about an error in cn.MOPS : could not find symbol "recursive" in environment of
... Could you run "traceback()" right after the error occurred and tell me the result of it? It seems like an error that does not come from cn.mops. Btw. "getReadCountsFromBAM" is just a "convenience function".. you can also use other methods to obtain the read count matrix. Regards, Günter ...
written 3 months ago by Günter Klambauer370
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Comment: C: How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
... Hello Amal, Any results that do not come from "referencecn.mops" do not make sense, since you only have two samples. If there is a CNV in one of the two samples, it is randomly assigned to one of the two... The assumption of cn.mops (including exomecn.mops) is that the majority of samples has copy ...
written 3 months ago by Günter Klambauer370
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Answer: A: parameter "refSeqName" in function "getReadCountsFromBAM"
... Just to make it visible also here... Something like the following typically works for human genomes and runs the function for chr1-22: X <- getReadCountsFromBAM(BAMFiles,refSeqName=as.character(1:22),WL=1000, mode="paired") If your sequence names are "chr1", "chr2" rather than "1", "2", then: ...
written 3 months ago by Günter Klambauer370
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Comment: C: How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
... I think your code for filtering the DNA segments does not work. I give you code how to do this on the data that comes with cn.MOPS: library(cn.mops) data(cn.mops) idx <- apply(values(XRanges),1, function(x) !all(x < 70)) XRangesSmall <- XRanges[idx, ] The code above removes DNA segmen ...
written 4 months ago by Günter Klambauer370

Latest awards to Günter Klambauer

Scholar 29 days ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: R code for cn.mops
Scholar 29 days ago, created an answer that has been accepted. For A: Finding structural analogs with Rchemcpp
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: R code for cn.mops -- if a chromosome does not have CNV ?
Scholar 15 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 15 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 16 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 16 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 22 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 22 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package

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