User: ns

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ns0
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Posts by ns

<prev • 7 results • page 1 of 1 • next >
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Answer: A: Somaticsignature NMF problem
... > rowSums(motifMatrix(snpvr_motif, group = "study", normalize = FALSE)) CA A.A CA A.C CA A.G CA A.T CA C.A CA C.C CA C.G CA C.T CA G.A CA G.C CA G.G CA G.T CA T.A CA T.C CA T.G CA T.T CG A.A CG A.C CG A.G CG A.T CG C.A CG C.C      15      4      8      5      6      9      7      6      5      1 ...
written 2.7 years ago by ns0
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Comment: C: Somaticsignature NMF problem
... Hi Julian, I checked my data table, and I do not have any studies with no  mutation calls (studies are in the columns).  I do have rows where the trinucleotide motifs are present that have 0 values.  See the example below   DJFS_1 DJFS_10 DJFS_100 DJFS_102 DJFS_107 ...
written 2.7 years ago by ns0
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Somaticsignature NMF problem
... Hello,  I am trying to run somaticsignatures on mutation data.   When I run the commands: snpvr_mm = motifMatrix(snpvr_motif, group = "study", normalize = TRUE) gof_nmf = identifySignatures(snpvr_mm, 4, decomposition = nmfDecomposition) I get the following error: Error: NMF::nmf - Input matrix ...
somaticsignatures nmf written 2.7 years ago by ns0 • updated 2.0 years ago by grimmmmer0
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Comment: C: SomaticSignatures plotSamples error
... Updating Bioconductor helped solve the problem. Thanks! ...
written 3.1 years ago by ns0
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Comment: C: SomaticSignatures plotSamples error
... Hi Julian, Since this is the only error I get, and no plots are made, I am not sure how to provide you with more details. The error "Error in if (debug) { : argument is of length zero" is seen with all Plot functions in SomaticSignatures. Using sessionInfo()  I have the output below, incase I am ...
written 3.1 years ago by ns0
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SomaticSignatures plotSamples error
... Hello,  I am using somaticsignatures to determine the mutation signatures post NMF decomposition in my samples. When I use the following commands: snpvr = with(snp, VRanges(seqnames = Chromosome, ranges = IRanges(Start_position, End_position), ref = Reference_Allele, alt = Tumor_Seq_Allele2, stud ...
somaticsignatures plotsamples written 3.1 years ago by ns0
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Comment: C: Problems using intansv...
... Hi Phill, I am using intansv and am running into a similar problem.  I was wondering if you figured out how to get around it? Thanks Natalie ...
written 4.5 years ago by ns0

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