Entering edit mode
Scott Ochsner
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300
@scott-ochsner-599
Last seen 10.3 years ago
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