[BioC] SomaticSignatures: could not find function "motifMatrix"

[Julian Gehring]

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/SomaticSignatures/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
>
> --
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>
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