User: Günter Klambauer

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480
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Austria
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http://www.bioinf.jku....
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2 months ago
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5 years, 3 months ago
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Posts by Günter Klambauer

<prev • 71 results • page 1 of 8 • next >
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Comment: C: about the runs with cn.mops
... Hello Bogdan, You should go with the CNVs in the slot "cnvs()". The integer copy numbers in the slot "cnvr()" are the average integer copy numbers in the whole region. Since the region is larger than the individual CNVs, in fact the region is a union of all CNVs that occur there, the average copy n ...
written 9 weeks ago by Günter Klambauer480
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Comment: C: about the runs with cn.mops
... The segmentation slot contains also normal ("CN2") segments, i.e. segment that do not contain a copy number variation. So, you should expect to find CN2 there. The "median" and "mean" are the median and mean signed individual I/NI (sI/NI) calls across the joined segments (cn.mops supplies and sI/NI ...
written 11 weeks ago by Günter Klambauer480
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Answer: A: about the runs with cn.mops
... Hello Bogdan,   Slot "segmentation": This contains the whole chromosome split into adjacent windows by breakpoints. This means that the initial windows, in which you counted the reads (e.g. 1000 bp), are joined to form longer segments. For each segment and sample, the inferred copy number is rep ...
written 11 weeks ago by Günter Klambauer480
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Answer: A: cn.MOPS - reporting log normalized read counts as table
... There is a hidden function called ".makeLogRatios" that you can apply to the cn.mops result object: library(cn.mops) data(cn.mops) res <- cn.mops(XRanges) logRatios <- cn.mops:::.makeLogRatios(res) as.data.frame(logRatios)   Regards, Günter ...
written 4 months ago by Günter Klambauer480
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Answer: A: How to combine CNVDetectionResult objects in cn.mops package
... Unfortunately I did not include a functionality like that. For the slot "cnvs" and "segmentation", I think, you just have to concatenate the results. For the "cnvr" slot, a union of the regions in the "cnvs" slot would be necessary! Regards, günter ...
written 4 months ago by Günter Klambauer480
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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 5 months ago by Günter Klambauer480
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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 5 months ago by Günter Klambauer480
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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 5 months ago by Günter Klambauer480
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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 7 months ago by Günter Klambauer480
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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 7 months ago by Günter Klambauer480

Latest awards to Günter Klambauer

Teacher 5 months 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 5 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: R code for cn.mops
Teacher 7 months 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 7 months ago, created an answer that has been accepted. For A: Finding structural analogs with Rchemcpp
Scholar 7 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 21 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 21 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
Scholar 2.4 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.4 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package

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