I want to convert ensembl ID to gene symbol using biomart.
My ensemble ID are write with the version like this:
ENSG00000066322.11 ENSG00000066336.10 ENSG00000066379.13
I have two problems: 1) Which the right version of ensembl to use for version of genome GRCh38.d1.vd1
2) How can extract from buiomart.
ensembl = useMart( host="dec2017.archive.ensembl.org",biomart="ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl" ) genemap <- getBM( attributes = c("ensembl_gene_id", "hgnc_symbol"), filters = "ensembl_gene_id", values = data$ensembl, mart = ensembl )
> sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=it_IT.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] gplots_3.0.1 genefilter_1.60.0 limma_3.34.9 [4] biomaRt_2.34.2 reshape2_1.4.3 RColorBrewer_1.1-2 [7] ggplot2_2.2.1 pheatmap_1.0.10 DESeq2_1.18.1 [10] SummarizedExperiment_1.8.1 DelayedArray_0.4.1 matrixStats_0.53.1 [13] Biobase_2.38.0 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 [16] IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0 [19] GenomicDataCommons_1.5.3 magrittr_1.5 loaded via a namespace (and not attached): [1] bitops_1.0-6 bit64_0.9-7 progress_1.1.2 httr_1.3.1 [5] tools_3.4.4 backports_1.1.2 utf8_1.1.4 R6_2.2.2 [9] KernSmooth_2.23-15 rpart_4.1-13 Hmisc_4.1-1 DBI_1.0.0 [13] lazyeval_0.2.1 colorspace_1.3-2 nnet_7.3-12 tidyselect_0.2.4 [17] gridExtra_2.3 prettyunits_1.0.2 bit_1.1-14 curl_3.2 [21] compiler_3.4.4 cli_1.0.0 htmlTable_1.12 xml2_1.2.0 [25] caTools_1.17.1 scales_0.5.0 checkmate_1.8.5 readr_1.1.1 [29] rappdirs_0.3.1 stringr_1.3.1 digest_0.6.15 foreign_0.8-70 [33] XVector_0.18.0 base64enc_0.1-3 pkgconfig_2.0.1 htmltools_0.3.6 [37] htmlwidgets_1.2 rlang_0.2.1 rstudioapi_0.7 RSQLite_2.1.1 [41] bindr_0.1.1 jsonlite_1.5 BiocParallel_1.12.0 gtools_3.5.0 [45] acepack_1.4.1 dplyr_0.7.5 RCurl_1.95-4.10 GenomeInfoDbData_1.0.0 [49] Formula_1.2-3 Matrix_1.2-14 Rcpp_0.12.17 munsell_0.4.3 [53] stringi_1.2.2 yaml_2.1.19 zlibbioc_1.24.0 plyr_1.8.4 [57] grid_3.4.4 blob_1.1.1 gdata_2.18.0 crayon_1.3.4 [61] lattice_0.20-35 splines_3.4.4 annotate_1.56.2 hms_0.4.2 [65] locfit_1.5-9.1 knitr_1.20 pillar_1.2.3 geneplotter_1.56.0 [69] XML_3.98-1.11 glue_1.2.0 latticeExtra_0.6-28 data.table_1.11.4 [73] gtable_0.2.0 purrr_0.2.5 assertthat_0.2.0 xtable_1.8-2 [77] survival_2.42-3 tibble_1.4.2 AnnotationDbi_1.40.0 memoise_1.1.0 [81] bindrcpp_0.2.2 cluster_2.0.7-1