Repitools/ClusterPlots
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I'm following the Repitools_vignette instruction guide (http://www.bio conductor.org/packages/devel/bioc/vignettes/Repitools/inst/doc/Repitoo ls_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')Err or: 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.
BSgenome BSgenome Repitools BSgenome BSgenome Repitools • 1.7k views
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@vincent-j-carey-jr-4
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Your software needs to be updated. I tried biocLite() with your version of R Using R version 2.13.0, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: [1] "Repitools" Please wait... Warning message: In getDependencies(pkgs, dependencies, available, lib) : package 'Repitools' is not available (for R version 2.13.0 Patched) Please upgrade your R to the current release, 2.14 and install Repitools using biocLite in that R. You will then have an Repitools with version >= 1.0 and if problems persist, please post full details. On Tue, Nov 8, 2011 at 7:09 AM, gillian [guest] <guest@bioconductor.org>wrote: > > 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')E rror: > 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Chao-Jen Wong ▴ 580
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Last seen 9.3 years ago
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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@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.bio conductor.org/packages/devel/bioc/vignettes/Repitools/inst/doc/Repitoo ls_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')Err or: 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. _______________________________________________ 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 -- 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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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.b ioconductor.org/packages/devel/bioc/vignettes/Repitools/inst/doc/Repit ools_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')Er ror: 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. > > _______________________________________________ > 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 > > -- > 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 > > _______________________________________________ > 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 ---------- Prof. Dr. Mark Robinson Bioinformatics Institute of Molecular Life Sciences University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland v: +41 44 635 4848 f: +41 44 635 6898 e: mark.robinson at imls.uzh.ch o: Y32-J-34 w: http://tiny.cc/mrobin
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