[BioC] Help with loading newly created custom annotation db into R session

[Ochsner, Scott A]

Dear list,

I'm following up with my install progress to complete this thread. After following the directions from the R Installation and Administration manual I downloaded Rtools minus the cygwin .dlls and edited my path to look as below:

PATH=c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGw\bin;C:\Perl\bin;c:\cygwin\bin; others...

As I already had an install of cygwin I added c:\cygwin\bin to the PATH as directed.  I then attempted to perform the install from the Command Prompt as follows:  

C:\Program Files\R\R-2.8.0\bin>R CMD INSTALL "c:\\Documents and Settings\\sochsner\\Desktop\\Zcustom.db"

This worked only after I updated cygwin.  

Thanks for the help,


Scott 
-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Monday, January 05, 2009 10:59 AM
To: Ochsner, Scott A
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Help with loading newly created custom annotation db into R session

Hi Scott,

You first need to install the package. Information can be found in the R-FAQ for windows:

http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install-packages-into-libraries-in-this-version_003f

Or you can have the win-builder do it for you (also at this link).

Best,

Jim



Ochsner, Scott A wrote:
> Dear list,
> 
> How do I load a custom annotation package into an R session?  I've 
> created a custom annotation database by following the steps laid out 
> in the SQLForge vignette using the gui version of R with windows XP.  Up until now, all I've had to do to load an annotation package into an R session is to use the convenient drop down menus within the gui to retrieve the package from BioC followed by library(package name.db).  I am at a loss as
to what to do with the new annotation package I've created which is sitting on my desktop.  I know I need to place the file into the correct path, I'm just not sure where or how.  I've looked at the list serve but have been unable to find a thread dealing with what I feel is probably a no brainer to
most users.
> 
>> library(AnnotationDbi)
>> openVignette()
>> read.table("C:\\DOCUME~1\\sochsner\\Desktop\\ZcustomIDs.txt",header=F
>> )[1:5,]
>                V1     V2
> 1 DR_UNI_CAND_A01  57935
> 2 DR_UNI_CAND_A01  57935
> 3 DR_UNI_CAND_A02 402842
> 4 DR_UNI_CAND_A02 402842
> 5 DR_UNI_CAND_A03 493624
>> ZcustomIDs<-"C:\\DOCUME~1\\sochsner\\Desktop\\ZcustomIDs.txt"
>> makeZEBRAFISHCHIP_DB(affy=FALSE,prefix="Zcustom",fileName=ZcustomIDs,
>> baseMapType="eg",outputDir="C:\\DOCUME~1\\sochsner\\Desktop",version=
>> "1.0.0",manufacturer="custom",chipName="Zebrafish custom array")
> Loading required package: RSQLite
> Loading required package: DBI
> baseMapType is eg
> Prepending Metadata
> Creating Genes table
> Appending Probes
> Found 0 Probe Accessions
> Appending Gene Info
> Found 4401 Gene Names
> Found 4401 Gene Symbols
> Appending Chromosomes
> Appending RefSeq
> Appending Pubmed
> Appending Unigene
> Appending ChrLengths
> Appending 3 GO tables
> Appending 3 GO ALL tables
> Appending KEGG
> Appending EC
> Appending Chromosome Locations
> Appending Pfam
> Appending Prosite
> Appending Alias
> Appending Ensembl
> Appending Uniprot
> Appending Zfin
> Appending Metadata
> 
> 
> Creating package in C:\DOCUME~1\sochsner\Desktop/Zcustom.db
>> sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
> States.1252;LC_MONETARY=English_United 
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] RSQLite_0.7-1       DBI_0.2-4           zebrafish.db0_2.2.5 AnnotationDbi_1.4.0 Biobase_2.2.0 
> 
> Scott A. Ochsner, Ph.D.
> Molecular and Cellular Biology
> Baylor College of Medicine
> Houston, TX. 77030
> phone: 713-798-6227
> 
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--
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662