How to specify the version for Plants.ensemble ?

[Sherry520]

I need to annote DEGs for Zea Maize of version 38, however the latest version is 52. My code is: plants <- useEnsembl(biomart = "plants_mart",host = "http://plants.ensembl.org",version = 38) However, it is not applicable to plants. listEnsemblArchives() can only get human information. Can you provide a code for plants? Error log: Error: Specified Ensembl version is not available. Use listEnsemblArchives() to view available versions.

sessionInfo()

R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936 LC_MONETARY=Chinese (Simplified)_China.936 [4] LC_NUMERIC=C LC_TIME=Chinese (Simplified)_China.936

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] ggpubr_0.4.0 ggplot2_3.3.5 WGCNA_1.69 fastcluster_1.1.25 dynamicTreeCut_1.63-1 pheatmap_1.0.12
[7] openxlsx_4.2.3 gdtools_0.2.3 UpSetR_1.4.0 biomaRt_2.46.3

loaded via a namespace (and not attached): [1] readxl_1.3.1 uuid_0.1-4 backports_1.2.0 Hmisc_4.4-2 BiocFileCache_1.14.0
[6] systemfonts_1.0.1 plyr_1.8.6 splines_4.0.2 crosstalk_1.1.0.1 digest_0.6.27
[11] foreach_1.5.1 htmltools_0.5.1.1 GO.db_3.12.1 fansi_0.4.1 magrittr_2.0.1
[16] checkmate_2.0.0 memoise_1.1.0 cluster_2.1.0 doParallel_1.0.16 remotes_2.4.0
[21] matrixStats_0.58.0 officer_0.3.16 askpass_1.1 prettyunits_1.1.1 jpeg_0.1-8.1
[26] colorspace_2.0-0 blob_1.2.1 rappdirs_0.3.1 haven_2.3.1 xfun_0.19
[31] dplyr_1.0.4 callr_3.5.1 crayon_1.3.4 jsonlite_1.7.2 impute_1.64.0
[36] survival_3.1-12 iterators_1.0.13 glue_1.4.2 rvg_0.2.5 gtable_0.3.0
[41] webshot_0.5.2 car_3.0-10 pkgbuild_1.2.0 BiocGenerics_0.36.0 abind_1.4-5
[46] scales_1.1.1 DBI_1.1.0 rstatix_0.7.0 miniUI_0.1.1.1 Rcpp_1.0.5
[51] xtable_1.8-4 progress_1.2.2 htmlTable_2.1.0 foreign_0.8-80 bit_4.0.4
[56] preprocessCore_1.52.0 Formula_1.2-4 stats4_4.0.2 htmlwidgets_1.5.3 httr_1.4.2
[61] RColorBrewer_1.1-2 ellipsis_0.3.1 pkgconfig_2.0.3 XML_3.99-0.5 farver_2.0.3
[66] nnet_7.3-14 dbplyr_2.1.0 tidyselect_1.1.0 labeling_0.4.2 rlang_0.4.10
[71] manipulateWidget_0.10.1 later_1.1.0.1 AnnotationDbi_1.52.0 cellranger_1.1.0 munsell_0.5.0
[76] tools_4.0.2 cli_2.2.0 generics_0.1.0 RSQLite_2.2.1 devEMF_4.0-2
[81] export_0.3.0 broom_0.7.5 evaluate_0.14 stringr_1.4.0 fastmap_1.1.0
[86] processx_3.4.5 knitr_1.30 bit64_4.0.5 zip_2.1.1 rgl_0.105.13
[91] purrr_0.3.4 mime_0.9 xml2_1.3.2 compiler_4.0.2 rstudioapi_0.13
[96] curl_4.3 png_0.1-7 ggsignif_0.6.1 tibble_3.0.4 stringi_1.5.3
[101] ps_1.5.0 forcats_0.5.1 stargazer_5.2.2 lattice_0.20-41 Matrix_1.2-18
[106] vctrs_0.3.6 pillar_1.4.7 lifecycle_1.0.0 BiocManager_1.30.10 data.table_1.13.4
[111] flextable_0.6.3 httpuv_1.5.5 R6_2.5.0 latticeExtra_0.6-29 promises_1.1.1
[116] rio_0.5.26 gridExtra_2.3 IRanges_2.24.1 codetools_0.2-16 assertthat_0.2.1
[121] openssl_1.4.3 rprojroot_2.0.2 withr_2.3.0 S4Vectors_0.28.1 parallel_4.0.2
[126] hms_0.5.3 grid_4.0.2 rpart_4.1-15 tidyr_1.1.3 rmarkdown_2.6
[131] carData_3.0-4 Biobase_2.50.0 shiny_1.6.0 base64enc_0.1-3

[grimbough]

Unfortunately Ensembl doesn't provide and Archive for plants version 38. The have 37 and 40. You can see a full list of available archives in the "Archive Sites" section of https://plants.ensembl.org

You can use one of those archives with something like this:

library(biomaRt)

ensembl_plants_40 <- useMart(host = "https://eg40-plants.ensembl.org/", 
                          biomart = "plants_mart", 
                          dataset = "zmays_eg_gene")