Question: Help with loading newly created custom annotation db into R session
0
gravatar for Scott Ochsner
10.8 years ago by
Scott Ochsner300
Scott Ochsner300 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
annotation go gui zebrafish probe • 1.1k views
ADD COMMENTlink modified 10.8 years ago by James W. MacDonald51k • written 10.8 years ago by Scott Ochsner300
Answer: Help with loading newly created custom annotation db into R session
0
gravatar for James W. MacDonald
10.8 years ago by
United States
James W. MacDonald51k wrote:
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=ZcustomID s,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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
ADD COMMENTlink written 10.8 years ago by James W. MacDonald51k
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@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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
ADD REPLYlink written 10.8 years ago by Scott Ochsner300
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