User: Günter Klambauer

Reputation:
400
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Trusted
Location:
Austria
Website:
http://www.bioinf.jku....
Last seen:
3 days, 17 hours ago
Joined:
4 years, 10 months ago
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Posts by Günter Klambauer

<prev • 66 results • page 1 of 7 • next >
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Answer: A: using cn.MOPS on WES data GERMLINE-TUMOR
... Hello Bogdan, The code is ok until "exomecn.mops". In a tumor vs. reference setting, I recommend to use "referencecn.mops", which also works for exome sequencing data. Regards, Günter ...
written 3 days ago by Günter Klambauer400
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Answer: A: getReadCountsFromBAM and paired-end reads
... Dear Alexandre, We have changed the read-counting procedure due to errors that were reported by several users in the last Bioc release. For simplicity, we have used the read-counting function of "exomecn.mops" which worked well empirically. However, for some purposes (such as whole genome sequencin ...
written 3 days ago by Günter Klambauer400
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Answer: A: Conflict in cnvr and cnvs result from cn.mops
... Sorry for the late response - I thought we clarified this via email. The segments in the CNVR slot are a union of the individual CNVs. For example, if individual A has a CNV in segments 3 and 4, and individual B has a CNV in segment 4 and 5, the CNVR-slot will contain a CNV-region spanning the thre ...
written 21 days ago by Günter Klambauer400
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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 8 weeks ago by Günter Klambauer400
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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 8 weeks ago by Günter Klambauer400
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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 8 weeks ago by Günter Klambauer400
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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 8 weeks ago by Günter Klambauer400
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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 8 weeks ago by Günter Klambauer400
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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 3 months ago by Günter Klambauer400
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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 4 months ago by Günter Klambauer400

Latest awards to Günter Klambauer

Scholar 8 weeks ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: R code for cn.mops
Scholar 8 weeks ago, created an answer that has been accepted. For A: Finding structural analogs with Rchemcpp
Teacher 8 weeks 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 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 17 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 17 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 23 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 23 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package

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