Question: SomaticSignatures plotSamples error
gravatar for ns
3.1 years ago by
United States
ns0 wrote:


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, study = Tumor_Sample_Barcode, refCount = (Coverage-Count), altCount = Count ))
snpvr_ucsc = ucsc(snpvr)
sort(table(snpvr_ucsc$study), decreasing = TRUE)
snpvr_motifs = mutationContext(snpvr_ucsc, BSgenome.Hsapiens.UCSC.hg19, unify = TRUE)
snpvr_mm = motifMatrix(snpvr_motifs, group = "study", normalize = FALSE)

n_sigs = 6
gof_nmf = identifySignatures(snpvr_mm, n_sigs, decomposition = nmfDecomposition)



I am getting the following error message:

Error in if (debug) { : argument is of length zero


Can you please let me know what might be the problem?




ADD COMMENTlink written 3.1 years ago by ns0

Can you please provide a full, reproducible example of your problem ( see )?

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Julian Gehring1.3k

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 using the wrong version of any of the packages.

R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggplot2_2.1.0                     BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.34.1                  
 [4] rtracklayer_1.26.3                SomaticSignatures_2.2.3           Biobase_2.26.0                   
 [7] VariantAnnotation_1.12.9          Rsamtools_1.18.3                  Biostrings_2.34.1                
[10] XVector_0.6.0                     GenomicRanges_1.18.4              GenomeInfoDb_1.2.5               
[13] IRanges_2.0.1                     S4Vectors_0.4.0                   BiocGenerics_0.12.1              
[16] reshape_0.8.5                    

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3         AnnotationDbi_1.28.2    backports_1.0.2         base64enc_0.1-3         BatchJobs_1.6          
 [6] BBmisc_1.9              BiocParallel_1.0.3      biomaRt_2.22.0          biovizBase_1.14.1       bitops_1.0-6           
[11] brew_1.0-6              checkmate_1.7.4         chron_2.3-47            cluster_2.0.4           codetools_0.2-14       
[16] colorspace_1.2-6        data.table_1.9.6        DBI_0.4                 dichromat_2.0-0         digest_0.6.9           
[21] doParallel_1.0.10       fail_1.3                foreach_1.4.3           foreign_0.8-66          Formula_1.2-1          
[26] GenomicAlignments_1.2.2 GenomicFeatures_1.18.7  GGally_1.0.1            ggbio_1.14.0            graph_1.44.1           
[31] grid_3.1.2              gridBase_0.4-7          gridExtra_0.9.1         gtable_0.2.0            Hmisc_3.17-4           
[36] iterators_1.0.8         labeling_0.3            lattice_0.20-33         latticeExtra_0.6-28     magrittr_1.5           
[41] Matrix_1.2-6            munsell_0.4.3           NMF_0.20.6              nnet_7.3-12             OrganismDbi_1.8.1      
[46] pcaMethods_1.56.0       pkgmaker_0.22           plyr_1.8.3              proxy_0.4-15            RBGL_1.42.0            
[51] RColorBrewer_1.1-2      Rcpp_0.12.4             RCurl_1.95-4.8          registry_0.3            reshape2_1.4.1         
[56] rngtools_1.2.4          rpart_4.1-10            RSQLite_1.0.0           scales_0.4.0            sendmailR_1.2-1        
[61] splines_3.1.2           stringi_1.0-1           stringr_1.0.0           survival_2.39-2         tools_3.1.2            
[66] XML_3.98-1.4            xtable_1.8-2            zlibbioc_1.12.0        

Please let me know if this helps, or if I should provide any more information.



ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by ns0

You are running a very outdated version of Bioconductor which also means that none of the installed packages has been supported for over a year. Could you consider upgrading your Bioconductor installation, as described in the help pages, and see if the issue still persists?

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Julian Gehring1.3k

Updating Bioconductor helped solve the problem.


ADD REPLYlink written 3.1 years ago by ns0
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