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, 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)
plotSamples(gof_nmf)
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?
Thanks!
Can you please provide a full, reproducible example of your problem ( see https://bioconductor.org/help/support/posting-guide )?
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) locale: [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_1.12.0Please let me know if this helps, or if I should provide any more information.
Natalie
Hi,
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?
Updating Bioconductor helped solve the problem.
Thanks!