[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.

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
>
> --
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>
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