User: Julian Gehring

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Julian Gehring1.3k
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Posts by Julian Gehring

<prev • 218 results • page 1 of 22 • next >
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Comment: C: Somatic Signature only SNV supported
... The vignette subsets for the SNV substitutions with sca_data = unname(subset(sca_data, Variant_Type %in% "SNP")) which is missing in your example. Is there a particular reason why you want to skip this step? Without this subsetting, the input contains indels as well which are not supported - and thi ...
written 7 weeks ago by Julian Gehring1.3k
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Comment: C: Somatic Signature only SNV supported
... Could you also add the output of the 'sessionInfo()' command? ...
written 7 weeks ago by Julian Gehring1.3k
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Comment: C: Somatic Signature only SNV supported
... Can you please provide a full, reproducible example of your analysis, including all the code that you ran up to the first error and the output of the sessionInfo command? Thanks. ...
written 7 weeks ago by Julian Gehring1.3k
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Comment: C: nmf function not working
... Thank you for the report. I have not been able to reproduce this issue with the same package versions as you have. Could you please post a complete example that I can rerun (from the starting of the R session until the error occurs) together with a complete output of the sessionInfo command? ...
written 3 months ago by Julian Gehring1.3k
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Comment: C: nmf function not working
... Please read the posting guide and provide the required details. ...
written 5 months ago by Julian Gehring1.3k
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Comment: C: SomaticSignatures: Compare my signatures with published COSMIC datasets
... "On another note, when using functions plotObservedSpectrum, plotFittedSpectrum I get an error " n too large, allowed maximum for palette Set3 is 12”. I think this is because the package is limited to 12 colours so i don't get an output with the remaining samples." The default colour palette define ...
written 15 months ago by Julian Gehring1.3k
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Comment: C: SomaticSignatures: Compare my signatures with published COSMIC datasets
... If I understood your approach correctly, the different correlations with the signatures from the two published data sets due to reasons outlined in my second comment. You may get a better overview by plotting your estimated signatures and the signatures of both data sets - this is often more informa ...
written 15 months ago by Julian Gehring1.3k
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Comment: C: SomaticSignatures: Compare my signatures with published COSMIC datasets
... "Seem that the correlation between data(signature21) and data(signature30) seem to be quite different although our results seem to concur with data(signature21) more. It seems like S18 from  data(signature21) is more correlated with Signature8 or Signature3 from data(signature30).  Could the names o ...
written 15 months ago by Julian Gehring1.3k
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Comment: C: SomaticSignatures: Compare my signatures with published COSMIC datasets
... "Briefly, we have ~80 samples under 4 conditions (groups) and have inferred 7 signatures for these for which we are trying to find out the specific signature per group." I'm not sure if I understand this correctly: If you have grouped your variant calls into 4 groups during the analysis, you can't ...
written 15 months ago by Julian Gehring1.3k
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Comment: C: Trouble while concatenating VRanges object ()
... This may be caused by the content of your VCF files, but without knowing how they look like, it will be hard to provide a solution. In order to narrow down the problem, can you please: Try to simplify the example: Do you need all 8 VCFs to reproduce the error? Does it happen with any combination ...
written 15 months ago by Julian Gehring1.3k

Latest awards to Julian Gehring

Popular Question 17 months ago, created a question with more than 1,000 views. For Looping over entries of a GRanges object
Scholar 2.6 years ago, created an answer that has been accepted. For A: motifMatrix input object type, confused VRange and GRange
Scholar 2.6 years ago, created an answer that has been accepted. For A: How do I split GRange object (set of genomic ranges with 2 metadata column) by c
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: How do I split GRange object (set of genomic ranges with 2 metadata column) by c
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: How do I split GRange object (set of genomic ranges with 2 metadata column) by c
Scholar 2.9 years ago, created an answer that has been accepted. For A: How do I split GRange object (set of genomic ranges with 2 metadata column) by c
Scholar 3.1 years ago, created an answer that has been accepted. For A: SomaticSignatures : change order of x-axis in plotMutationSpectrum
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: SomaticSignatures : change order of x-axis in plotMutationSpectrum
Scholar 3.3 years ago, created an answer that has been accepted. For A: SomaticSignature - what samples contributed to each signature
Scholar 3.4 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Scholar 3.4 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Scholar 3.4 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Centurion 3.8 years ago, created 100 posts.
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: import wig to coverage
Scholar 3.9 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Scholar 4.1 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Scholar 4.2 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: SomaticSignatures: Compare my datas with validated mutational signatures

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