User: Günter Klambauer

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Posts by Günter Klambauer

<prev • 57 results • page 1 of 6 • next >
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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 7 days ago by Günter Klambauer300
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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 7 days ago by Günter Klambauer300
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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 12 days ago by Günter Klambauer300
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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 weeks ago by Günter Klambauer300
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Comment: C: Call CNV in population with large depth variance
... Hello Xiao, The program determines the window length automatically based upon the sample with the lowest number of reads (lowest coverage). However, I advise to do some calculations and set this parameter by hand such that on average about 50-100 reads map to each window (segment). The average num ...
written 5 weeks ago by Günter Klambauer300
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Answer: A: Call CNV in population with large depth variance
... Hello Xiao Zhang, Yes, clustering the samples with respect to sequencing depth is certainly advisable. You can include the higher coverage samples when you analyze the low coverage ones. Let me explain this further: Let's say the low coverage samples are A, the medium coverage samples are B, and th ...
written 5 weeks ago by Günter Klambauer300
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Comment: C: How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
... Hello Amal, There is a workaround: Go back to the initial "getReadCountsFromBAM" and use a small segment size, e.g. "WL=50". Then you get a read count matrix with segments/windows along the whole genome. Remove rows with zero read counts across all samples (these are the DNA segments that were not ...
written 6 weeks ago by Günter Klambauer300
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Answer: A: How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
... Hello Amal, The reason for this behaviour of cn.mops is that you used the "whole genome sequencing" script. The function "getReadCountsFromBAM" partitions the genome into equally sized windows and counts how many reads are in these windows. However, you have targeted sequencing data and you should ...
written 6 weeks ago by Günter Klambauer300
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Answer: A: Input (X) data type is not numeric if read from GRanges obj
... Hello Mohammad, Your comments are very welcome - as always! Thanks for flagging this issue. I will make the changes to cn.mops accordingly. Regards, Günter On 2016-12-28 07:20, Mohammad Alkhamis [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: ...
written 8 weeks ago by Günter Klambauer300
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Answer: A: cn.mops: NA in the output of referencecn.mops
... Hello Radek, Thanks for using cn.mops! This functionality should actually work. The return object should contain the integer copy numbers of the cases. Could you please upgrade to the most recent version of R / Bioconductor / cn.mops and check if the problem persists? If yes, could you give me ...
written 3 months ago by Günter Klambauer300

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
Scholar 12 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 13 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 13 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 19 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 19 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package

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