Entering edit mode
Francois Marchildon
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20
@francois-marchildon-14131
Last seen 2.1 years 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