User: TRASA

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TRASA0
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Posts by TRASA

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Error in YAPSA::annotate_intermut_dist_cohort
... Hi I tried to use the annotate_intermut_dist_cohort command from the YAPSA package on my VRangesList. However, I got following error message.i > vr_dist <- annotate_intermut_dist_cohort(vrl, in_mode="min", in_verbose = TRUE) Error in `[[<-`(`*tmp*`, name, value = c(1e+10, 2489564 ...
yapsa written 6 weeks ago by TRASA0
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negative AD value interfering with readVcfasVRanges
... Hi I am trying to convert Vcf files to VRanges objects. However, I get following Error message readVcfAsVRanges(vcf1) Error in validObject(.Object) : invalid class "VRanges" object: 'refDepth' must be non-negative I found this support post: https://stat.ethz.ch/pipermail/bioconductor/2 ...
variantannotation written 6 weeks ago by TRASA0 • updated 29 days ago by Michael Lawrence11k
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Error in NMF estimation
... Hi I would like to perform de novo mutational signature extraction. I am trying to follow the vignette of the MutationalPattern package. I managed to create the matrix for my samples. However, I encounter problems when I try to estiamte the number of mutational signatures in my samples. Here my cod ...
nmf mutationalpatterns written 8 weeks ago by TRASA0
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Error Message in signeR
... Hi all I have a list of VCF files, where I would like to assess the mutational signature from. First, I needed to combine the vcf's in one matrix according to signeR vignette. mut = matrix(ncol=96,nrow=0) for(i in list_vcf) { vo = readVcf(i, "hg19") # sample name (should pick ...
getseq signer written 9 weeks ago by TRASA0 • updated 9 weeks ago by renan.valieris10
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Comment: C: Somatic Signature only SNV supported
... No, there is no reason. I must have completely missed that. Sorry for bothering you with such a stupid mistake... ...
written 9 months ago by TRASA0
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Comment: C: Somatic Signature only SNV supported
... I loaded following libraries library(SomaticSignatures) library(SomaticCancerAlterations) library(BSgenome.Hsapiens.1000genomes.hs37d5) And then run following code (including output) > sca_data = unlist(scaLoadDatasets()) > > sca_data$study = factor(gsub("(.*)_(.*)", "\\1", toupper(na ...
written 9 months ago by TRASA0
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Somatic Signature only SNV supported
...   Hi I am using the Bioconductor package SomaticSignatures. Since I am very new to NSG anaysis, I tried to reproduce the example used in the Read.me of the package. However, I run into some problems when extracting the sequence context (Section 4.2). I got the following error message. Error in m ...
somaticsignatures written 9 months ago by TRASA0

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