I am trying to retrieve Oryza sativa protein coding genes with their annotations. When running this code months ago, it worked fine. Now when I run it, I get a data frame with the list of gene IDs, chromosome names, start and stop positions, but only NAs in the description column. I need some help figuring out how to get the gene annotations again!
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("biomaRt", version = "3.8")
library("biomaRt")
rice_mart <- useMart("plants_mart",
dataset="osativa_eg_gene",
host="plants.ensembl.org")
rice_genes <- getBM(attributes = c("ensembl_gene_id",
"chromosome_name",
"start_position",
"end_position",
"description"),
filters = "biotype",
values = "protein_coding",
mart=rice_mart)
sessionInfo() R version 3.5.3 (2019-03-11) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.4
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale: [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt2.38.0 GenomicRanges1.34.0 GenomeInfoDb1.18.2 IRanges2.16.0 S4Vectors0.20.1
[6] BiocGenerics0.28.0
loaded via a namespace (and not attached):
[1] Rcpp1.0.1 BiocManager1.30.4 compiler3.5.3 XVector0.22.0
[5] prettyunits1.0.2 bitops1.0-6 tools3.5.3 progress1.2.0
[9] zlibbioc1.28.0 digest0.6.18 bit1.1-14 RSQLite2.1.1
[13] memoise1.1.0 pkgconfig2.0.2 rlang0.3.4 DBI1.0.0
[17] rstudioapi0.10 curl3.3 yaml2.2.0 xfun0.6
[21] GenomeInfoDbData1.2.0 stringr1.4.0 httr1.4.0 knitr1.22
[25] hms0.4.2 bit640.9-7 Biobase2.42.0 R62.4.0
[29] AnnotationDbi1.44.0 XML3.98-1.19 blob1.1.1 magrittr1.5
[33] assertthat0.2.1 stringi1.4.3 RCurl1.95-4.12 crayon1.3.4