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I want to get the annotation for a list of genes whose identifier is ensembl, but when I try to use select it give an error. Then I used the example from the documentation to get some annotations and the error was the same. I do not understand what is wrong
BiocManager::install("EnsDb.Hsapiens.v86", force=TRUE)
library(EnsDb.Hsapiens.v86)
edb <- EnsDb.Hsapiens.v86
library(dplyr)
select(edb, keys = c("BCL2", "BCL2L11"), keytype = "GENENAME",
columns = c("GENEID", "GENENAME", "TXID", "TXBIOTYPE"))
##ERROR
Error in UseMethod("select") :
no applicable method for 'select' applied to an object of class "EnsDb"
sessionInfo( )
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
Matrix products: default
locale:
[1] LC_COLLATE=Spanish_Spain.1252
[2] LC_CTYPE=Spanish_Spain.1252
[3] LC_MONETARY=Spanish_Spain.1252
[4] LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils
[7] datasets methods base
other attached packages:
[1] dplyr_1.0.7 EnsDb.Hsapiens.v86_2.99.0
[3] ensembldb_2.16.4 AnnotationFilter_1.16.0
[5] GenomicFeatures_1.44.2 AnnotationDbi_1.54.1
[7] Biobase_2.52.0 GenomicRanges_1.44.0
[9] GenomeInfoDb_1.28.4 IRanges_2.26.0
[11] S4Vectors_0.30.2 BiocGenerics_0.38.0
loaded via a namespace (and not attached):
[1] MatrixGenerics_1.4.3 httr_1.4.2
[3] bit64_4.0.5 assertthat_0.2.1
[5] BiocManager_1.30.16 BiocFileCache_2.0.0
[7] blob_1.2.2 GenomeInfoDbData_1.2.6
[9] Rsamtools_2.8.0 yaml_2.2.1
[11] progress_1.2.2 pillar_1.6.4
[13] RSQLite_2.2.8 lattice_0.20-45
[15] glue_1.4.2 digest_0.6.28
[17] XVector_0.32.0 Matrix_1.3-4
[19] XML_3.99-0.8 pkgconfig_2.0.3
[21] biomaRt_2.48.3 zlibbioc_1.38.0
[23] purrr_0.3.4 BiocParallel_1.26.2
[25] tibble_3.1.5 KEGGREST_1.32.0
[27] generics_0.1.1 ellipsis_0.3.2
[29] cachem_1.0.6 SummarizedExperiment_1.22.0
[31] lazyeval_0.2.2 magrittr_2.0.1
[33] crayon_1.4.1 memoise_2.0.0
[35] fansi_0.5.0 xml2_1.3.2
[37] tools_4.1.1 prettyunits_1.1.1
[39] hms_1.1.1 BiocIO_1.2.0
[41] lifecycle_1.0.1 matrixStats_0.61.0
[43] stringr_1.4.0 DelayedArray_0.18.0
[45] Biostrings_2.60.2 compiler_4.1.1
[47] rlang_0.4.12 grid_4.1.1
[49] RCurl_1.98-1.5 rstudioapi_0.13
[51] rjson_0.2.20 rappdirs_0.3.3
[53] bitops_1.0-7 restfulr_0.0.13
[55] DBI_1.1.1 curl_4.3.2
[57] R6_2.5.1 GenomicAlignments_1.28.0
[59] rtracklayer_1.52.1 fastmap_1.1.0
[61] bit_4.0.4 utf8_1.2.2
[63] filelock_1.0.2 ProtGenerics_1.24.0
[65] stringi_1.7.5 Rcpp_1.0.7
[67] vctrs_0.3.8 png_0.1-7
[69] dbplyr_2.1.1 tidyselect_1.1.1
For example