[BioC] Repitools/ClusterPlots
Mark Robinson
mark.robinson at imls.uzh.ch
Wed Nov 9 09:13:17 CET 2011
Hi Gillian,
An oversight on our part -- those functions were inadvertently dropped. Version 1.0.1 should work better. Apologies for the hiccup.
Regards,
Mark
On 08.11.2011, at 19:29, Wong, Chao-Jen wrote:
> Hi, Gilian
>
> As Vince mentioned, the Repitools package doesn't exist in R 2.13 branch, but in R 2.14. It is just recently released as version 1.0.0. Anyhow, clusterPlots() was deleted from the package prior to its release and the authors haven't taken out the examples related to clusters from the vignette, which, indeed, is confusing. I don't know authors' plan on their cluster functions, but certainly I would suggest the authors to update their vignette according to their current changes to the package.
>
> Chao-Jen
>
> ----- Original Message -----
> From: "gillian [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, gillianscience at yahoo.co.uk
> Sent: Tuesday, November 8, 2011 4:09:04 AM
> Subject: [BioC] Repitools/ClusterPlots
>
>
> I'm following the Repitools_vignette instruction guide (http://www.bioconductor.org/packages/devel/bioc/vignettes/Repitools/inst/doc/Repitools_vignette.pdf) and I'm stuck with the part where you need to use clusterPlots.
>
>> From the guide it seems like clusterPlots is part of Repitools, but I have Repitools installed (featureScores, for example, works fine), and clusterPlots doesn't work:
>
>> cpUnscaled=clusterPlots(fsUnscaled,n.clusters=1,plot.type='line')Error: could not find function "clusterPlots"
>
> So it looks like I don't have whatever library it's a part of installed, but I can't tell what that is. I've got pretty much everything from the session info of the guide installed:
> Their Session Info:
> This vignette was created in:
> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> locale:
> [1] LC_CTYPE=en_AU.UTF-8
> [3] LC_TIME=en_AU.UTF-8
> [5] LC_MONETARY=C
> [7] LC_PAPER=en_AU.UTF-8
> [9] LC_ADDRESS=C
> [11] LC_MEASUREMENT=en_AU.UTF-8
> LC_NUMERIC=C
> LC_COLLATE=en_AU.UTF-8
> LC_MESSAGES=en_AU.UTF-8
> LC_NAME=C
> LC_TELEPHONE=C
> LC_IDENTIFICATION=C
> attached base packages:
> [1] grid
> stats
> graphics
> [8] base
> grDevices utils
> other attached packages:
> [1] BSgenome.Hsapiens36bp.UCSC.hg18mappability_1.0
> [2] gplots_2.8.0
> [3] caTools_1.12
> [4] bitops_1.0-4.1
> [5] gdata_2.8.2
> [6] gtools_2.6.2
> [7] Ringo_1.16.0
> [8]
> Matrix_0.999375-50
>
> [9] lattice_0.19-26
> [10] limma_3.8.2
> [11] RColorBrewer_1.0-2
> [12] Biobase_2.12.1
> [13] edgeR_2.2.5
> [14] BSgenome.Hsapiens.UCSC.hg18_1.3.17
> [15] BSgenome_1.20.0
> [16] Biostrings_2.20.1
> [17] Repitools_0.99.1
> [18] GenomicRanges_1.4.6
> [19] IRanges_1.10.4
>
>
>
>
>
>
>
>
> loaded via a namespace (and not attached):
> [1] annotate_1.30.0
> AnnotationDbi_1.14.1
> DBI_0.2-5
> [4] genefilter_1.34.0
> RSQLite_0.9-4
> splines_2.13.0
> [7] survival_2.36-9
> xtable_1.5-6
>
>
> but still no luck. Anyone got any idea where I can find clusterPlots, or what I'm missing?
>
> Thanks,
>
> Gillian
>
>
> -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
> [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
> [7] LC_PAPER=en_GB.utf8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] gplots_2.10.1 KernSmooth_2.23-5 caTools_1.12
> [4] bitops_1.0-4.1 gdata_2.8.2 gtools_2.6.2
> [7] Ringo_1.16.0 Matrix_1.0-1 lattice_0.19-26
> [10] limma_3.8.1 RColorBrewer_1.0-5 Biobase_2.12.1
> [13] edgeR_2.2.6 Rsamtools_1.4.3 Biostrings_2.20.0
> [16] GenomicRanges_1.4.3 IRanges_1.10.0 Repitools_1.1.0
>
> loaded via a namespace (and not attached):
> [1] annotate_1.30.1 AnnotationDbi_1.14.1 BSgenome_1.20.0
> [4] DBI_0.2-5 genefilter_1.34.0 RSQLite_0.9-4
> [7] splines_2.13.0 survival_2.36-9 tools_2.13.0
> [10] xtable_1.6-0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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> --
> Chao-Jen Wong
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Avenue N., M1-B514
> PO Box 19024
> Seattle, WA 98109
> 206.667.4485
> cwon2 at fhcrc.org
>
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----------
Prof. Dr. Mark Robinson
Bioinformatics
Institute of Molecular Life Sciences
University of Zurich
Winterthurerstrasse 190
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Switzerland
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