User: Julian Gehring

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Julian Gehring1.3k
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Posts by Julian Gehring

<prev • 219 results • page 2 of 22 • next >
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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 2.0 years 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 2.1 years 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 2.2 years 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 2.2 years 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 2.4 years 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 2.4 years ago by Julian Gehring1.3k
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Answer: A: Somaticsignature NMF problem
... The error results from the fact that some mutational motifs have not been occurred in any of the samples, i.e. some of the rows of the motif matrix are fully zero. This prevents the decomposition of the matrix with the NMF. I'll try to capture this explicitly in the package and provide a more inform ...
written 2.6 years ago by Julian Gehring1.3k
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Comment: C: Somaticsignature NMF problem
... How many mutations do you have per sample/study? I.e. what does rowSums(motifMatrix(snpvr_motif, group = "study", normalize = FALSE)) return? ...
written 2.6 years ago by Julian Gehring1.3k
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Comment: C: Somaticsignature NMF problem
... Judging from "Error: NMF::nmf - Input matrix x contains at least one null or NA-filled row.", I would suspect that your input 'snpvr_mm' contains a full row, i.e. study, without any mutations. Can you check if this is the case? It is not possible to narrow it down further from the distance without k ...
written 2.6 years ago by Julian Gehring1.3k
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Comment: C: Annotate VCFs with Cosmic (ExAC etc.) fields
... If you have your variants as VRanges objects, methods like match, %in%, %over% and friends also consider the alternative allele (see the help page): 'match(x)’: Like GRanges ‘match’, except matches on the combination of chromosome, start, width, and *alt*. Personally, and just in case you are not ...
written 2.9 years ago by Julian Gehring1.3k

Latest awards to Julian Gehring

Popular Question 11 months ago, created a question with more than 1,000 views. For Looping over entries of a GRanges object
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Looping over entries of a GRanges object
Scholar 3.4 years ago, created an answer that has been accepted. For A: motifMatrix input object type, confused VRange and GRange
Scholar 3.4 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 3.4 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 3.6 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
Scholar 3.6 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
Scholar 3.8 years ago, created an answer that has been accepted. For A: SomaticSignatures : change order of x-axis in plotMutationSpectrum
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: SomaticSignatures : change order of x-axis in plotMutationSpectrum
Scholar 4.1 years ago, created an answer that has been accepted. For A: SomaticSignature - what samples contributed to each signature
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
Scholar 4.2 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Centurion 4.6 years ago, created 100 posts.
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: import wig to coverage
Scholar 4.6 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Scholar 4.9 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Scholar 4.9 years ago, created an answer that has been accepted. For A: SomaticSignatures: Compare my datas with validated mutational signatures
Teacher 4.9 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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