User: Günter Klambauer

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540
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Austria
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http://www.bioinf.jku....
Last seen:
6 months ago
Joined:
7 years, 4 months ago
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Posts by Günter Klambauer

<prev • 90 results • page 1 of 9 • next >
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Comment: C: cn.mops on CRAM files
... Yes, you can stack them column-wise (samples) or row-wise (genomic segments). This is exactly what GRanges objects are meant for: easy handling of genomic information data. ...
written 6 months ago by Günter Klambauer540
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Answer: A: cn.mops on CRAM files
... Havent worked with CRAM files, but it should be possible to directly get read counts from them. Will check for solutions. Maybe anyone from the community could help with this? Regards, Guenter ...
written 6 months ago by Günter Klambauer540
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Answer: A: mosdepth output into cn.mops?
... Dear Philipp, Yes it is very well possible and also reasonable to use the output of mosdepth as input for cn.mops. There is only one thing to check: does mosdepth return "depth of coverage" or "readcounts"? From the GRanges object it seems that these are integer numbers and therefore read counts. ...
written 8 months ago by Günter Klambauer540
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Answer: C: tumor vs control: multiple samples
... Just use the default referencecn.mops function. Submit multiple tumor samples in the according input argument, and also multiple control samples in the according input argument. referencecn.mops will calculate an appropriate control sample and compare each tumor sample against the control.   ...
written 12 months ago by Günter Klambauer540
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Answer: A: cn.MOPs: Error in value[[3L]](cond) :
... Ok, this is a problem either with your BAM files or with Rsamtools with the function "scanBam". Please contact the maintainers of Rsamtools. ...
written 17 months ago by Günter Klambauer540
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Answer: A: cn.MOPs: Error in value[[3L]](cond) :
... I think this is not a problem of cn.mops but of an internally used function (Rsamtools?). Could you run "traceback" right after the error occurs and post the result here. Please check if for each BAM file, there exists an BAI (index) file. This can be generated using samtools Regards, Günter ...
written 17 months ago by Günter Klambauer540
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Answer: A: Doubt about WL in cn.mops
... Hi, This is an intrinsic problem of the read count data. If you have a small WL, the counts are low and you will easily get large fold-changes: Imagine that most samples of a readcount of 1 and one sample has a read count of 2. Then this would be a strong signal in terms of fold-changes (2-fold cha ...
written 17 months ago by Günter Klambauer540
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Comment: C: Doubt about WL in cn.mops
... see below   ...
written 17 months ago by Günter Klambauer540
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Answer: A: cn.mops: interpreting output when returnPosterior=TRUE
... 1. There is no additional column, but an extra slot (resCNMOPS@something) that returns the three dimensional array of posterior probs (segments x samples x copynumberclasses). 2. The default thresholds of cn.MOPS should work fine. If you have a validation set with known CNVs you should adjust the p ...
written 19 months ago by Günter Klambauer540
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Answer: A: best way to normalize for differences in sample read depth: normalize genome vs
... Hi, Yes, the function "cn.mops" internally also applies normalization. I just added the function "normalizeGenome" and "normalizeChromosome" for Users who want to normalize by hand. So, there is no difference between first applying the normalization function and then running cn.mops with "norm=0" ( ...
written 21 months ago by Günter Klambauer540

Latest awards to Günter Klambauer

Scholar 12 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Teacher 2.5 years 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 2.5 years ago, created an answer that has been accepted. For A: Finding structural analogs with Rchemcpp
Scholar 2.5 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.5 years ago, created an answer that has been accepted. For A: refSeqName issue in cn.MOPS
Teacher 2.5 years 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 2.5 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.6 years ago, created an answer that has been accepted. For A: Finding structural analogs with Rchemcpp
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: R code for cn.mops
Teacher 2.6 years 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 2.6 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 3.9 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 3.9 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 3.9 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 3.9 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 4.4 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 4.4 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package

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