LRBaseDbi error
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Entering edit mode
@francois-marchildon-14131
Last seen 8 days ago
Rockefeller University, New York City

Dear bioconductor,

I'm experiencing difficulties to construct a LRBaseDb object with AnnotationHub. I'm trying to follow the package vignette but I am running into an error. See example below.

Any help would be appreciated.

Franc

library('AnnotationHub')
library('LRBaseDbi')
y <- AnnotationHub()
data <- query(y, c("LRBaseDb", "Mus musculus"))[[1]]
keytypes(data)

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘keytypes’ for signature ‘"character"’

sessionInfo()
 [1] LRBaseDbi_2.2.0             AnnotationHub_3.0.1        
 [3] BiocFileCache_2.0.0         dbplyr_2.1.1               
 [5] hpar_1.34.0                 dorothea_1.4.1             
 [7] tibble_3.1.4                tidygraph_1.2.0            
 [9] msigdbr_7.4.1               pals_1.7                   
[11] rnaseqtools_0.1.3           plyr_1.8.6                 
[13] tidyr_1.1.3                 ReactomePA_1.36.0          
[15] dplyr_1.0.7                 ComplexHeatmap_2.8.0       
[17] stringr_1.4.0               colorRamps_2.3             
[19] VennDiagram_1.6.20          futile.logger_1.4.3        
[21] clusterProfiler_4.0.5       reactome.db_1.76.0         
[23] org.Mm.eg.db_3.13.0         AnnotationDbi_1.54.1       
[25] ggrepel_0.9.1               biomaRt_2.48.3             
[27] ggplot2_3.3.5               pheatmap_1.0.12            
[29] RColorBrewer_1.1-2          DESeq2_1.32.0              
[31] SummarizedExperiment_1.22.0 Biobase_2.52.0             
[33] MatrixGenerics_1.4.3        matrixStats_0.60.1         
[35] GenomicRanges_1.44.0        GenomeInfoDb_1.28.2        
[37] IRanges_2.26.0              S4Vectors_0.30.0           
[39] BiocGenerics_0.38.0         devtools_2.4.2             
[41] usethis_2.0.1
LRBaseDbi AnnotationHub • 32 views
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