Loading library with name in a variable
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Entering edit mode
@patrick-schorderet-6081
Last seen 6.5 years ago
United States

Dear all,

 

I am trying to load a database, which name is in a variable (I actually ask the user to provide the name of the database he needs). Does any body know if this is even possible??

TaxonDatabaseKG <- "TxDb.Mmusculus.UCSC.mm10.knownGene"

TaxonDatabaseKG
[1] "TxDb.Mmusculus.UCSC.mm10.knownGene"

library(TaxonDatabaseKG)        # I'd like this to be similar as library(TxDb.Mmusculus.UCSC.mm10.knownGene)

 

I keep getting an error message:

Error in library(TaxonDatabaseKG) :  there is no package called ‘TaxonDatabaseKG’

 

Thanks for any help

 

 

 

 

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] VennDiagram_1.6.9       gtools_3.4.1            edgeR_3.8.5            
 [4] limma_3.22.1            GenomicAlignments_1.2.1 Rsamtools_1.18.2       
 [7] Biostrings_2.34.1       XVector_0.6.0           GenomicRanges_1.18.3   
[10] AnnotationDbi_1.28.1    GenomeInfoDb_1.2.3      IRanges_2.0.1          
[13] S4Vectors_0.4.0         Biobase_2.26.0          BiocGenerics_0.12.1    

loaded via a namespace (and not attached):
 [1] base64enc_0.1-2    BatchJobs_1.5      BBmisc_1.8         BiocParallel_1.0.0
 [5] bitops_1.0-6       brew_1.0-6         checkmate_1.5.0    codetools_0.2-9   
 [9] DBI_0.3.1          digest_0.6.4       fail_1.2           foreach_1.4.2     
[13] iterators_1.0.7    RSQLite_1.0.0      sendmailR_1.2-1    stringr_0.6.2     
[17] tools_3.1.2        zlibbioc_1.12.0   

 

 

library characters • 999 views
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Entering edit mode

ok, I got it: FYI:

library(...,character.only = TRUE)

And use get(...) to access it.

 

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