[BioC] Repitools/ClusterPlots

Tue Nov 8 19:29:22 CET 2011

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   

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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