EnsDb.Rnorvegicus for Rnor6
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keremwai • 0
@keremwai-23766
Last seen 14 months ago

Is there a package version of EnsDb.Rnorvegicus that is based on the newer version of Rattus Norvegicus reference Rnor6? All I could find is v79 which is based on older reference Rnor5. Thanks Kerem

annotation db reference rnor6 • 303 views
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Guido Hooiveld ★ 3.0k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …

Yes, please have a look at the excellent ENSEMBL-based annotation packages Johannes Rainer provides through the AnnotationHub!

See below for some code to get you started. Note that I am using ENSEMBL v100, but if needed you can easily create a EnsDb for another ENSEMBL version!

> # if needed, install required libraries.
> BiocManager::install(c("AnnotationHub", "ensembldb", "AnnotationForge")
> 
> library(AnnotationHub)
> library(ensembldb)
> library(AnnotationForge)
>
> # start an AnnotationHub instance/connection.
> ah <- AnnotationHub()
snapshotDate(): 2020-04-27
> 
> # query for availabel Rat Ensembl databases
> EnsDb.rat <- query(ah, c("EnsDb", "Rattus norvegicus"))
> EnsDb.rat
AnnotationHub with 14 records
# snapshotDate(): 2020-04-27
# $dataprovider: Ensembl
# $species: Rattus norvegicus
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH53239"]]' 

            title                                  
  AH53239 | Ensembl 87 EnsDb for Rattus Norvegicus 
  AH53743 | Ensembl 88 EnsDb for Rattus Norvegicus 
  AH56709 | Ensembl 89 EnsDb for Rattus Norvegicus 
  AH57792 | Ensembl 90 EnsDb for Rattus Norvegicus 
  AH60814 | Ensembl 91 EnsDb for Rattus Norvegicus 
  ...       ...                                    
  AH69261 | Ensembl 96 EnsDb for Rattus norvegicus 
  AH73956 | Ensembl 97 EnsDb for Rattus norvegicus 
  AH75088 | Ensembl 98 EnsDb for Rattus norvegicus 
  AH78871 | Ensembl 99 EnsDb for Rattus norvegicus 
  AH79776 | Ensembl 100 EnsDb for Rattus norvegicus
>
> # Fetch the v100 EnsDb and put it in the cache.
> EnsDb.rat <- EnsDb.rat[["AH79776"]]
>
> #check
> columns(EnsDb.rat)
 [1] "DESCRIPTION"         "ENTREZID"            "EXONID"             
 [4] "EXONIDX"             "EXONSEQEND"          "EXONSEQSTART"       
 [7] "GCCONTENT"           "GENEBIOTYPE"         "GENEID"             
   <<snip>>
> 
> 
> # Now copy, and install the database locally.
> # By doing so, you can just quickly load the library next time.
> # see: ?makeEnsembldbPackage
> 
> #set working dir to store the relaively large files.
> setwd("E:\\myDir")
>
> #copy databse from the cache to working dir
> file.copy(AnnotationHub::cache(ah["AH79776"]), "./EnsDb.rat.sqlite")
 [1] TRUE
>
> # now make it a package. Change name and email accordingly
> makeEnsembldbPackage("EnsDb.rat.sqlite", version="0.0.1",
+     maintainer = "First Name <first.last@mydomain.com>",
+     author = "First Name <first.last@mydomain.com>",
+     destDir=".", license="Artistic-2.0")
Creating package in ./EnsDb.Rnorvegicus.v100 
[1] TRUE
>
>
> # install package in R.  
> # note modifed name of created directory (not EnsDb.rat... but EnsDb.Rnorvegicus.v100)
> install.packages("./EnsDb.Rnorvegicus.v100", type = "source", repos = NULL)
* installing *source* package 'EnsDb.Rnorvegicus.v100' ...
** using staged installation
* DONE (EnsDb.Rnorvegicus.v100)
> 
> #check: 
> library(EnsDb.Rnorvegicus.v100)
> EnsDb.Rnorvegicus.v100
EnsDb for Ensembl:
|Backend: SQLite
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.3.5
|Creation time: Sat May  2 05:29:36 2020
|ensembl_version: 100
|ensembl_host: localhost
|Organism: Rattus norvegicus
|taxonomy_id: 10116
|genome_build: Rnor_6.0
|DBSCHEMAVERSION: 2.1
| No. of genes: 32883.
| No. of transcripts: 41078.
|Protein data available.
>
> columns(EnsDb.Rnorvegicus.v100)
 [1] "DESCRIPTION"         "ENTREZID"            "EXONID"             
  <<snip>>      
[37] "UNIPROTID"           "UNIPROTMAPPINGTYPE" 
>
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Below some code to create 'an-easy-to-transport' package from it (didn't fit in answer above).

> # If needed, create packages for offline installation
> # in other R installations.
> # Use library devtools for this!
>
> library(devtools)
> 
> # To create a binary (ZIP) 
Loading required package: usethis
> build("EnsDb.Rnorvegicus.v100", binary = TRUE)

-  installing to library 'C:/TMP_R/RtmpGSRmpU/temp_libpath3ec4539149f1' (555ms)
  packaged installation of 'EnsDb.Rnorvegicus.v100' as EnsDb.Rnorvegicus.v100_0.0.1.zip
-  DONE (EnsDb.Rnorvegicus.v100)

[1] "E:/xxxx/EnsDb/EnsDb.Rnorvegicus.v100_0.0.1.zip"
> 
> # To create a source package (TAR.GZ)
> build("EnsDb.Rnorvegicus.v100", binary = FALSE)
    -  building 'EnsDb.Rnorvegicus.v100_0.0.1.tar.gz'
 [1] "E:/xxxx/EnsDb/EnsDb.Rnorvegicus.v100_0.0.1.tar.gz"
> 
> 
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] devtools_2.3.0               usethis_1.6.1               
 [3] EnsDb.Rnorvegicus.v100_0.0.1 AnnotationForge_1.30.1      
 [5] ensembldb_2.12.1             AnnotationFilter_1.12.0     
 [7] GenomicFeatures_1.40.0       AnnotationDbi_1.50.0        
 [9] Biobase_2.48.0               GenomicRanges_1.40.0        
[11] GenomeInfoDb_1.24.2          IRanges_2.22.2              
[13] S4Vectors_0.26.1             AnnotationHub_2.20.0        
[15] BiocFileCache_1.12.0         dbplyr_1.4.4                
[17] BiocGenerics_0.34

You can then install the packages (see remarks James below). :-)

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Don't forget the installation!

install.packages("E:/xxxx/EnsDb/EnsDb.Rnorvegicus.v100_0.0.1.tar.gz", repos = NULL)
## on Windows do
install.packages("E:/xxxx/EnsDb/EnsDb.Rnorvegicus.v100_0.0.1.tar.gz", repos = NULL, type = "source")

And now you can load like any package.

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