Dear Sir/Madam, I have been working through your excellent vignette for the SomaticSignatures package (http://www.bioconductor.org/packages/devel/ bioc/vignettes/SomaticSignatures/inst/doc/SomaticSignatures- vignette.html ), but when I reach the motifMatrix step, the function appears to missing. Has motifMatrix been deprecated? Kind regards, Max -- output of sessionInfo(): R version 3.1.1 (2014-07-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] BSgenome.Hsapiens.UCSC.hg19_1.3.99 BSgenome_1.32.0 [3] SomaticCancerAlterations_1.0.0 stringr_0.6.2 [5] ggplot2_1.0.0 VariantAnnotation_1.10.5 [7] Rsamtools_1.16.1 Biostrings_2.32.1 [9] XVector_0.4.0 GenomicRanges_1.16.3 [11] GenomeInfoDb_1.0.2 IRanges_1.22.9 [13] SomaticSignatures_1.0.1 Biobase_2.24.0 [15] BiocGenerics_0.10.0 BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] AnnotationDbi_1.26.0 BatchJobs_1.3 BBmisc_1.7 [4] BiocParallel_0.6.1 biomaRt_2.20.0 biovizBase_1.12.1 [7] bitops_1.0-6 brew_1.0-6 checkmate_1.1 [10] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 [13] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 [16] doParallel_1.0.8 exomeCopy_1.10.0 fail_1.2 [19] foreach_1.4.2 Formula_1.1-2 GenomicAlignments_1.0.3 [22] GenomicFeatures_1.16.2 ggbio_1.12.8 grid_3.1.1 [25] gridBase_0.4-7 gridExtra_0.9.1 gtable_0.1.2 [28] gtools_3.4.1 Hmisc_3.14-4 iterators_1.0.7 [31] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-33 [34] munsell_0.4.2 NMF_0.20.5 pcaMethods_1.54.0 [37] pkgmaker_0.22 plyr_1.8.1 proto_0.3-10 [40] RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 [43] registry_0.2 reshape2_1.4 rngtools_1.2.4 [46] RSQLite_0.11.4 rtracklayer_1.24.2 scales_0.2.4 [49] sendmailR_1.1-2 splines_3.1.1 stats4_3.1.1 [52] survival_2.37-7 tools_3.1.1 XML_3.98-1.1 [55] xtable_1.7-3 zlibbioc_1.10.0 -- Sent via the guest posting facility at bioconductor.org.

Hi Max, You are using the release version of the SomaticSignatures package, but looking at the vignette of the developer version. The matching vignette is http://www.bioconductor.org/packages/devel/bioc/vignettes/SomaticSigna tures/inst/doc/SomaticSignatures-vignette.html or simply run browseVignettes(package = "SomaticSignatures") in your R session which will direct you to the correct version. Best wishes Julian On 21.07.2014 10:28, Max Salm [guest] wrote: > Dear Sir/Madam, > > I have been working through your excellent vignette for the SomaticSignatures package (http://www.bioconductor.org/packages/devel/ bioc/vignettes/SomaticSignatures/inst/doc/SomaticSignatures- vignette.html ), but when I reach the motifMatrix step, the function appears to missing. Has motifMatrix been deprecated? > > Kind regards, > > Max > > -- output of sessionInfo(): > > R version 3.1.1 (2014-07-10) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 > [2] LC_CTYPE=English_United Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] BSgenome.Hsapiens.UCSC.hg19_1.3.99 BSgenome_1.32.0 > [3] SomaticCancerAlterations_1.0.0 stringr_0.6.2 > [5] ggplot2_1.0.0 VariantAnnotation_1.10.5 > [7] Rsamtools_1.16.1 Biostrings_2.32.1 > [9] XVector_0.4.0 GenomicRanges_1.16.3 > [11] GenomeInfoDb_1.0.2 IRanges_1.22.9 > [13] SomaticSignatures_1.0.1 Biobase_2.24.0 > [15] BiocGenerics_0.10.0 BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.26.0 BatchJobs_1.3 BBmisc_1.7 > [4] BiocParallel_0.6.1 biomaRt_2.20.0 biovizBase_1.12.1 > [7] bitops_1.0-6 brew_1.0-6 checkmate_1.1 > [10] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 > [13] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 > [16] doParallel_1.0.8 exomeCopy_1.10.0 fail_1.2 > [19] foreach_1.4.2 Formula_1.1-2 GenomicAlignments_1.0.3 > [22] GenomicFeatures_1.16.2 ggbio_1.12.8 grid_3.1.1 > [25] gridBase_0.4-7 gridExtra_0.9.1 gtable_0.1.2 > [28] gtools_3.4.1 Hmisc_3.14-4 iterators_1.0.7 > [31] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-33 > [34] munsell_0.4.2 NMF_0.20.5 pcaMethods_1.54.0 > [37] pkgmaker_0.22 plyr_1.8.1 proto_0.3-10 > [40] RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 > [43] registry_0.2 reshape2_1.4 rngtools_1.2.4 > [46] RSQLite_0.11.4 rtracklayer_1.24.2 scales_0.2.4 > [49] sendmailR_1.1-2 splines_3.1.1 stats4_3.1.1 > [52] survival_2.37-7 tools_3.1.1 XML_3.98-1.1 > [55] xtable_1.7-3 zlibbioc_1.10.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

Hi Max, You are using the release version of the SomaticSignatures package, but looking at the vignette of the developer version. The matching vignette is http://www.bioconductor.org/packages/devel/bioc/vignettes/SomaticSigna tures/inst/doc/SomaticSignatures-vignette.html or simply run browseVignettes(package = "SomaticSignatures") in your R session which will direct you to the correct version. I renamed some of the functions in the developer version, but would always recommend to use the release version for your analysis, as you already did. Best wishes Julian On 21.07.2014 10:28, Max Salm [guest] wrote: > Dear Sir/Madam, > > I have been working through your excellent vignette for the SomaticSignatures package (http://www.bioconductor.org/packages/devel/ bioc/vignettes/SomaticSignatures/inst/doc/SomaticSignatures- vignette.html ), but when I reach the motifMatrix step, the function appears to missing. Has motifMatrix been deprecated? > > Kind regards, > > Max > > -- output of sessionInfo(): > > R version 3.1.1 (2014-07-10) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 > [2] LC_CTYPE=English_United Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] BSgenome.Hsapiens.UCSC.hg19_1.3.99 BSgenome_1.32.0 > [3] SomaticCancerAlterations_1.0.0 stringr_0.6.2 > [5] ggplot2_1.0.0 VariantAnnotation_1.10.5 > [7] Rsamtools_1.16.1 Biostrings_2.32.1 > [9] XVector_0.4.0 GenomicRanges_1.16.3 > [11] GenomeInfoDb_1.0.2 IRanges_1.22.9 > [13] SomaticSignatures_1.0.1 Biobase_2.24.0 > [15] BiocGenerics_0.10.0 BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.26.0 BatchJobs_1.3 BBmisc_1.7 > [4] BiocParallel_0.6.1 biomaRt_2.20.0 biovizBase_1.12.1 > [7] bitops_1.0-6 brew_1.0-6 checkmate_1.1 > [10] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 > [13] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 > [16] doParallel_1.0.8 exomeCopy_1.10.0 fail_1.2 > [19] foreach_1.4.2 Formula_1.1-2 GenomicAlignments_1.0.3 > [22] GenomicFeatures_1.16.2 ggbio_1.12.8 grid_3.1.1 > [25] gridBase_0.4-7 gridExtra_0.9.1 gtable_0.1.2 > [28] gtools_3.4.1 Hmisc_3.14-4 iterators_1.0.7 > [31] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-33 > [34] munsell_0.4.2 NMF_0.20.5 pcaMethods_1.54.0 > [37] pkgmaker_0.22 plyr_1.8.1 proto_0.3-10 > [40] RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 > [43] registry_0.2 reshape2_1.4 rngtools_1.2.4 > [46] RSQLite_0.11.4 rtracklayer_1.24.2 scales_0.2.4 > [49] sendmailR_1.1-2 splines_3.1.1 stats4_3.1.1 > [52] survival_2.37-7 tools_3.1.1 XML_3.98-1.1 > [55] xtable_1.7-3 zlibbioc_1.10.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

Hi Max, You are using the release version of the SomaticSignatures package, but looking at the vignette of the developer version. The matching vignette is http://www.bioconductor.org/packages/devel/bioc/vignettes/SomaticSigna tures/inst/doc/SomaticSignatures-vignette.html or simply run browseVignettes(package = "SomaticSignatures") in your R session which will direct you to the correct version. I renamed some of the functions in the developer version, but would always recommend to use the release version for your analysis, as you already did. Best wishes Julian On 21.07.2014 10:28, Max Salm [guest] wrote: > Dear Sir/Madam, > > I have been working through your excellent vignette for the SomaticSignatures package (http://www.bioconductor.org/packages/devel/ bioc/vignettes/SomaticSignatures/inst/doc/SomaticSignatures- vignette.html ), but when I reach the motifMatrix step, the function appears to missing. Has motifMatrix been deprecated? > > Kind regards, > > Max > > -- output of sessionInfo(): > > R version 3.1.1 (2014-07-10) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 > [2] LC_CTYPE=English_United Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] BSgenome.Hsapiens.UCSC.hg19_1.3.99 BSgenome_1.32.0 > [3] SomaticCancerAlterations_1.0.0 stringr_0.6.2 > [5] ggplot2_1.0.0 VariantAnnotation_1.10.5 > [7] Rsamtools_1.16.1 Biostrings_2.32.1 > [9] XVector_0.4.0 GenomicRanges_1.16.3 > [11] GenomeInfoDb_1.0.2 IRanges_1.22.9 > [13] SomaticSignatures_1.0.1 Biobase_2.24.0 > [15] BiocGenerics_0.10.0 BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.26.0 BatchJobs_1.3 BBmisc_1.7 > [4] BiocParallel_0.6.1 biomaRt_2.20.0 biovizBase_1.12.1 > [7] bitops_1.0-6 brew_1.0-6 checkmate_1.1 > [10] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 > [13] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 > [16] doParallel_1.0.8 exomeCopy_1.10.0 fail_1.2 > [19] foreach_1.4.2 Formula_1.1-2 GenomicAlignments_1.0.3 > [22] GenomicFeatures_1.16.2 ggbio_1.12.8 grid_3.1.1 > [25] gridBase_0.4-7 gridExtra_0.9.1 gtable_0.1.2 > [28] gtools_3.4.1 Hmisc_3.14-4 iterators_1.0.7 > [31] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-33 > [34] munsell_0.4.2 NMF_0.20.5 pcaMethods_1.54.0 > [37] pkgmaker_0.22 plyr_1.8.1 proto_0.3-10 > [40] RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 > [43] registry_0.2 reshape2_1.4 rngtools_1.2.4 > [46] RSQLite_0.11.4 rtracklayer_1.24.2 scales_0.2.4 > [49] sendmailR_1.1-2 splines_3.1.1 stats4_3.1.1 > [52] survival_2.37-7 tools_3.1.1 XML_3.98-1.1 > [55] xtable_1.7-3 zlibbioc_1.10.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >