User: Julian Gehring

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Julian Gehring1.3k
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Posts by Julian Gehring

<prev • 213 results • page 1 of 22 • next >
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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 10 weeks 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 10 weeks 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 10 weeks 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 10 weeks 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 10 weeks ago by Julian Gehring1.3k
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Comment: C: SomaticSignatures error when loading data
... Can you please have a look at https://master.bioconductor.org/help/support/posting-guide/ and provide a minimal example up to the point of the error rather than all commands you intend to run add a sessionInfo and traceback highlight which command actually failed ...
written 3 months ago by Julian Gehring1.3k
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Answer: A: plotMutationSpectrum Colour By Patient with Multiple Samples
... This is an interesting use case - it will not work out of the box, but we can make it happen. I have created a modified version of the plotMutationSpectrum function that has the extra functionality: library(SomaticSignatures) library(ggplot2) plotMutationSpectrumWithColorMapping <- function(vr ...
written 4 months ago by Julian Gehring1.3k
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Answer: A: SomaticSignatures package : motifMatrix function trouble
... In order to construct a matrix with the counts of mutational motifs, you need the variant calls annotated with the mutational context (the context column) and a grouping variable that is also present in your VRanges object. The grouping variable then defines the columns of your mutational matrix M, ...
written 5 months ago by Julian Gehring1.3k
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Comment: C: SomaticSignatures: Transcription Factor Specific Mutation Signature Enrichment
... The answers in this support forum are largely contributed by volunteers that do this during their free and personal time. Pushing for answers after five days, especially during the Easter weekend where many people have other commitments, is neither helpful nor encouraging. ...
written 7 months ago by Julian Gehring1.3k
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Comment: C: SomaticSignatures: Transcription Factor Specific Mutation Signature Enrichment
... I have trouble understanding the questions you are trying to answer. Could you please provide more context and, if possible, also some results that would help in understanding it better? Specifically, what do you mean with "tumor wise cases instead of certain areas" in question 1? Also, are you inte ...
written 7 months ago by Julian Gehring1.3k

Latest awards to Julian Gehring

Scholar 19 months ago, created an answer that has been accepted. For A: motifMatrix input object type, confused VRange and GRange
Scholar 19 months 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 19 months 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 21 months 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 21 months 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 2.0 years ago, created an answer with at least 3 up-votes. For A: SomaticSignatures : change order of x-axis in plotMutationSpectrum
Scholar 2.0 years ago, created an answer that has been accepted. For A: SomaticSignatures : change order of x-axis in plotMutationSpectrum
Scholar 2.3 years ago, created an answer that has been accepted. For A: SomaticSignature - what samples contributed to each signature
Scholar 2.3 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Scholar 2.3 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Scholar 2.4 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Centurion 2.8 years ago, created 100 posts.
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: import wig to coverage
Scholar 2.8 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Scholar 3.1 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Scholar 3.1 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Teacher 3.1 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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