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Hi, I am having issues with retrieving Zea mays genes dataset, could you please fix it?
library(biomaRt)
host = "https://plants.ensembl.org"
listMarts(host = host)
ensembl <- useEnsembl(biomart = "plants_mart", host = host)
ensembl |> listDatasets()
ensembl <- useDataset(dataset = "zmays_eg_gene", mart = ensembl)
################################
sessionInfo( )
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese (Simplified)_China.utf8 LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8
time zone: Asia/Shanghai
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.60.1
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 utf8_1.2.4 generics_0.1.3 xml2_1.3.6 RSQLite_2.3.7 stringi_1.8.4 hms_1.1.3 digest_0.6.37
[9] magrittr_2.0.3 fastmap_1.2.0 blob_1.2.4 jsonlite_1.8.8 progress_1.2.3 AnnotationDbi_1.66.0 GenomeInfoDb_1.40.1 DBI_1.2.3
[17] httr_1.4.7 purrr_1.0.2 fansi_1.0.6 UCSC.utils_1.0.0 Biostrings_2.72.1 httr2_1.0.3 cli_3.6.3 rlang_1.1.4
[25] crayon_1.5.3 dbplyr_2.5.0 XVector_0.44.0 Biobase_2.64.0 bit64_4.0.5 withr_3.0.1 cachem_1.1.0 tools_4.4.1
[33] memoise_2.0.1 dplyr_1.1.4 filelock_1.0.3 GenomeInfoDbData_1.2.12 BiocGenerics_0.50.0 curl_5.2.2 vctrs_0.6.5 R6_2.5.1
[41] png_0.1-8 stats4_4.4.1 lifecycle_1.0.4 BiocFileCache_2.12.0 zlibbioc_1.50.0 KEGGREST_1.44.1 stringr_1.5.1 S4Vectors_0.42.1
[49] IRanges_2.38.1 bit_4.0.5 pkgconfig_2.0.3 pillar_1.9.0 glue_1.7.0 tibble_3.2.1 tidyselect_1.2.1 rstudioapi_0.16.0
[57] compiler_4.4.1 prettyunits_1.2.0
This is amazing. Thank you so much