Question: Does GSEABase support organismDb objects?
0
gravatar for sandmann.t
2.3 years ago by
sandmann.t50
sandmann.t50 wrote:

Dear Martin,

thanks a lot for implementing the awesome GSEABase infrastructure. Especially the conversion between identifiers is something I use a lot. So far, I had been annotating my GeneSet objects by referencing orgDb objects (e.g. org.Mm.eg.db).

Once I noticed that there are the OrganismDb wrapper packages as well (e.g. Mus.musculus), I tried to use them instead, but without success (see below). 

If it's not me doing something wrong here, I just wanted to let you know - in case you were assuming that OrganismDb packages worked as well.

Best,

Thomas

> library(GSEABase)
> library(org.Mm.eg.db)

# referencing an orgDb object
> gs <- GeneSet(setName = "test", geneIds = "Trp53",
                geneIdType = SymbolIdentifier("org.Mm.eg.db"))
> gs
setName: test 
geneIds: Trp53 (total: 1)
geneIdType: Symbol (org.Mm.eg.db)
collectionType: Null 
details: use 'details(object)'

> geneIdType(gs) <- EntrezIdentifier()

> gs
setName: test 
geneIds: 22059 (total: 1)
geneIdType: EntrezId (org.Mm.eg.db)
collectionType: Null 
details: use 'details(object)'

# referencing the OrganismDb object instead
> gs <- GeneSet(setName = "test", geneIds = "Tp53",
                geneIdType = SymbolIdentifier("Mus.musculus"))

> gs
setName: test 
geneIds: Tp53 (total: 1)
geneIdType: Symbol (Mus.musculus)
collectionType: Null 
details: use 'details(object)'

> geneIdType(gs) <- EntrezIdentifier()
Error in .select(x, keys, columns, keytype, ...) : 
  You must provide a keytype argument
sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Mus.musculus_1.3.1                       TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 GO.db_3.4.1                              OrganismDbi_1.18.0                      
 [5] GenomicFeatures_1.28.3                   GenomicRanges_1.28.3                     GenomeInfoDb_1.12.2                      org.Mm.eg.db_3.4.1                      
 [9] GSEABase_1.38.0                          graph_1.54.0                             annotate_1.54.0                          XML_3.98-1.9                            
[13] AnnotationDbi_1.38.1                     IRanges_2.10.2                           S4Vectors_0.14.3                         Biobase_2.36.2                          
[17] BiocGenerics_0.22.0                      devtools_1.13.2                         

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11               BiocInstaller_1.26.0       compiler_3.4.0             XVector_0.16.0             bitops_1.0-6               tools_3.4.0               
 [7] zlibbioc_1.22.0            biomaRt_2.32.1             digest_0.6.12              bit_1.1-12                 lattice_0.20-35            RSQLite_2.0               
[13] memoise_1.1.0              tibble_1.3.3               pkgconfig_2.0.1            rlang_0.1.1                Matrix_1.2-10              DelayedArray_0.2.7        
[19] DBI_0.7                    rstudioapi_0.6             GenomeInfoDbData_0.99.0    rtracklayer_1.36.3         withr_1.0.2                Biostrings_2.44.1         
[25] grid_3.4.0                 bit64_0.9-7                RBGL_1.52.0                BiocParallel_1.10.1        blob_1.1.0                 matrixStats_0.52.2        
[31] GenomicAlignments_1.12.1   Rsamtools_1.28.0           SummarizedExperiment_1.6.3 xtable_1.8-2               RCurl_1.95-4.8          
gseabase • 395 views
ADD COMMENTlink written 2.3 years ago by sandmann.t50
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