Question: SomaticSignatures objects in new version
1
gravatar for Dave Wettmann
4.6 years ago by
United Kingdom
Dave Wettmann40 wrote:

Hello,

I'm looking at objects generated using the previous version of SomaticSignatures in the latest version.  The objects were generated as part of the example in the vignette but they now seem to produce errors when I try to plot them e.g. 

> plotSampleMap(sigs_nmf)
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘samples’ for signature ‘"list"’

Some of my own data objects I generated using the previous version (which functioned correctly) are also throwing similar errors when I try to use some of the plot functions.  Would it be best to downgrade to the previous version?

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] ggplot2_1.0.0                     SomaticCancerAlterations_1.0.0
 [3] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.34.0
 [5] rtracklayer_1.26.1                SomaticSignatures_2.1.0
 [7] synchronicity_1.1.4               bigmemory_4.4.6
 [9] BH_1.54.0-4                       bigmemory.sri_0.1.3
[11] Biobase_2.26.0                    VariantAnnotation_1.12.1
[13] Rsamtools_1.18.0                  Biostrings_2.34.0
[15] XVector_0.6.0                     GenomicRanges_1.18.1
[17] GenomeInfoDb_1.2.0                IRanges_2.0.0
[19] S4Vectors_0.4.0                   BiocGenerics_0.12.0

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3         AnnotationDbi_1.28.0    base64enc_0.1-2
 [4] BatchJobs_1.4           BBmisc_1.7              BiocParallel_1.0.0
 [7] biomaRt_2.22.0          biovizBase_1.14.0       bitops_1.0-6
[10] brew_1.0-6              checkmate_1.5.0         cluster_1.15.3
[13] codetools_0.2-9         colorspace_1.2-4        DBI_0.3.1
[16] dichromat_2.0-0         digest_0.6.4            doParallel_1.0.8
[19] exomeCopy_1.10.0        fail_1.2                foreach_1.4.2
[22] foreign_0.8-61          Formula_1.1-2           GenomicAlignments_1.2.0
[25] GenomicFeatures_1.18.1  GGally_0.4.8            ggbio_1.14.0
[28] graph_1.44.0            grid_3.1.1              gridBase_0.4-7
[31] gridExtra_0.9.1         gtable_0.1.2            Hmisc_3.14-5
[34] iterators_1.0.7         labeling_0.3            lattice_0.20-29
[37] latticeExtra_0.6-26     MASS_7.3-35             munsell_0.4.2
[40] NMF_0.20.5              nnet_7.3-8              OrganismDbi_1.8.0
[43] pcaMethods_1.56.0       pkgmaker_0.22           plyr_1.8.1
[46] proto_0.3-10            RBGL_1.42.0             RColorBrewer_1.0-5
[49] Rcpp_0.11.3             RCurl_1.95-4.3          registry_0.2
[52] reshape_0.8.5           reshape2_1.4            rngtools_1.2.4
[55] rpart_4.1-8             RSQLite_0.11.4          scales_0.2.4
[58] sendmailR_1.2-1         splines_3.1.1           stringr_0.6.2
[61] survival_2.37-7         tools_3.1.1             XML_3.98-1.1
[64] xtable_1.7-4            zlibbioc_1.12.0

 

somaticsignatures • 630 views
ADD COMMENTlink modified 4.6 years ago by James W. MacDonald50k • written 4.6 years ago by Dave Wettmann40
Answer: SomaticSignatures objects in new version
1
gravatar for Julian Gehring
4.6 years ago by
Julian Gehring1.3k
Julian Gehring1.3k wrote:

The SomaticSignatures package has a new major release (version 2.*.*) with additional features, a slightly modified user interface and a different data representation.  Overall, it still does the same as the 1.*.* version, but it may bring some incompatibilities - you have encountered that.

The main problem that you are facing: Before, we stored the signatures as a simple list.  While this got the job done, the new version of the package now uses MutationalSignatures objects. It is much clearer and easier to use.

Downgrading to the 1.*.* version of the package may solve your problem in the short run, but I do not recommend this:

  • For this to work, you would also have to downgrade your Bioconductor release from 3.0 to 2.15. This is outdated and not maintained any more.
  • Since the old version of Bioconductor is not maintained anymore, this also means that the old version of SomaticSignatures is not updated with patches etc.
  • Generally, the 2.*.* release of SomaticSignatures brings new and good features that I guess you want to have in the long run.

I can offer two solutions:

  • Rerun your analysis with the 2.*.* release of SomaticSignatures if possible. I strongly recommend this.
  • We can convert the data that you have from your old analysis (the simple lists) to the MutationalSignatures object.

A side note: I have updated the package since the 2.0.0 release - by now, you want the 2.2.1 or any newer version. Consider running biocLite("SomaticSignatures").

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Julian Gehring1.3k
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