Last updated: 2025-09-04
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 87b461f | Dave Tang | 2025-09-04 | Using biomaRt to get homologues |
To begin, install the {biomaRt} package.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("biomaRt")Load package.
suppressPackageStartupMessages(library(biomaRt))
packageVersion("biomaRt")[1] '2.64.0'List the available BioMart databases.
listMarts() biomart version
1 ENSEMBL_MART_ENSEMBL Ensembl Genes 115
2 ENSEMBL_MART_MOUSE Mouse strains 115
3 ENSEMBL_MART_SNP Ensembl Variation 115
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 115Connect to the selected BioMart database by using
useMart().
ensembl <- useMart("ENSEMBL_MART_ENSEMBL")
avail_datasets <- listDatasets(ensembl)
head(avail_datasets) dataset description
1 abrachyrhynchus_gene_ensembl Pink-footed goose genes (ASM259213v1)
2 acalliptera_gene_ensembl Eastern happy genes (fAstCal1.3)
3 acarolinensis_gene_ensembl Green anole genes (AnoCar2.0v2)
4 acchrysaetos_gene_ensembl Golden eagle genes (bAquChr1.2)
5 acitrinellus_gene_ensembl Midas cichlid genes (Midas_v5)
6 amelanoleuca_gene_ensembl Giant panda genes (ASM200744v2)
version
1 ASM259213v1
2 fAstCal1.3
3 AnoCar2.0v2
4 bAquChr1.2
5 Midas_v5
6 ASM200744v2Look for human datasets by searching the description column.
idx <- grep('human', avail_datasets$description, ignore.case = TRUE)
avail_datasets[idx, ] dataset description version
80 hsapiens_gene_ensembl Human genes (GRCh38.p14) GRCh38.p14Connect to the selected BioMart database and human dataset.
ensembl <- useMart("ensembl", dataset=avail_datasets[idx, 'dataset'])
ensemblObject of class 'Mart':
Using the ENSEMBL_MART_ENSEMBL BioMart database
Using the hsapiens_gene_ensembl datasetBuilding a query, requires three things:
Use listFilters() to show available filters.
avail_filters <- listFilters(ensembl)
head(avail_filters) name description
1 chromosome_name Chromosome/scaffold name
2 start Start
3 end End
4 band_start Band Start
5 band_end Band End
6 marker_start Marker StartUse listAttributes() to show available attributes.
avail_attributes <- listAttributes(ensembl)
head(avail_attributes) name description page
1 ensembl_gene_id Gene stable ID feature_page
2 ensembl_gene_id_version Gene stable ID version feature_page
3 ensembl_transcript_id Transcript stable ID feature_page
4 ensembl_transcript_id_version Transcript stable ID version feature_page
5 ensembl_peptide_id Protein stable ID feature_page
6 ensembl_peptide_id_version Protein stable ID version feature_pageLook for mouse homologues.
grep('homolog', avail_attributes$name, ignore.case = TRUE, value = TRUE) |>
grep('mmus', x = _, ignore.case = TRUE, value = TRUE) -> wanted_attr
wanted_attr <- c('ensembl_gene_id', wanted_attr)
wanted_attr [1] "ensembl_gene_id"
[2] "mmusculus_homolog_ensembl_gene"
[3] "mmusculus_homolog_associated_gene_name"
[4] "mmusculus_homolog_ensembl_peptide"
[5] "mmusculus_homolog_chromosome"
[6] "mmusculus_homolog_chrom_start"
[7] "mmusculus_homolog_chrom_end"
[8] "mmusculus_homolog_canonical_transcript_protein"
[9] "mmusculus_homolog_subtype"
[10] "mmusculus_homolog_orthology_type"
[11] "mmusculus_homolog_perc_id"
[12] "mmusculus_homolog_perc_id_r1"
[13] "mmusculus_homolog_goc_score"
[14] "mmusculus_homolog_wga_coverage"
[15] "mmusculus_homolog_orthology_confidence" ENSG00000206172 (HBA1).
my_gene <- 'ENSG00000206172'
getBM(
attributes = wanted_attr,
filters = "ensembl_gene_id",
values = my_gene,
mart = ensembl
) -> my_res
t(my_res) [,1]
ensembl_gene_id "ENSG00000206172"
mmusculus_homolog_ensembl_gene "ENSMUSG00000069919"
mmusculus_homolog_associated_gene_name "Hba-a1"
mmusculus_homolog_ensembl_peptide "ENSMUSP00000090897"
mmusculus_homolog_chromosome "11"
mmusculus_homolog_chrom_start "32233511"
mmusculus_homolog_chrom_end "32234465"
mmusculus_homolog_canonical_transcript_protein "ENSP00000322421"
mmusculus_homolog_subtype "Boreoeutheria"
mmusculus_homolog_orthology_type "ortholog_many2many"
mmusculus_homolog_perc_id "86.6197"
mmusculus_homolog_perc_id_r1 "86.6197"
mmusculus_homolog_goc_score "75"
mmusculus_homolog_wga_coverage "0"
mmusculus_homolog_orthology_confidence "1"
[,2]
ensembl_gene_id "ENSG00000206172"
mmusculus_homolog_ensembl_gene "ENSMUSG00000069917"
mmusculus_homolog_associated_gene_name "Hba-a2"
mmusculus_homolog_ensembl_peptide "ENSMUSP00000090895"
mmusculus_homolog_chromosome "11"
mmusculus_homolog_chrom_start "32246489"
mmusculus_homolog_chrom_end "32247298"
mmusculus_homolog_canonical_transcript_protein "ENSP00000322421"
mmusculus_homolog_subtype "Boreoeutheria"
mmusculus_homolog_orthology_type "ortholog_many2many"
mmusculus_homolog_perc_id "86.6197"
mmusculus_homolog_perc_id_r1 "86.6197"
mmusculus_homolog_goc_score "25"
mmusculus_homolog_wga_coverage "0"
mmusculus_homolog_orthology_confidence "0"
sessionInfo()R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.64.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] KEGGREST_1.48.1 xfun_0.52 bslib_0.9.0
[4] httr2_1.2.1 processx_3.8.6 Biobase_2.68.0
[7] callr_3.7.6 vctrs_0.6.5 tools_4.5.0
[10] ps_1.9.1 generics_0.1.4 curl_6.4.0
[13] stats4_4.5.0 tibble_3.2.1 AnnotationDbi_1.70.0
[16] RSQLite_2.4.2 blob_1.2.4 pkgconfig_2.0.3
[19] dbplyr_2.5.0 S4Vectors_0.46.0 lifecycle_1.0.4
[22] GenomeInfoDbData_1.2.14 compiler_4.5.0 stringr_1.5.1
[25] git2r_0.36.2 Biostrings_2.76.0 progress_1.2.3
[28] getPass_0.2-4 httpuv_1.6.16 GenomeInfoDb_1.44.1
[31] htmltools_0.5.8.1 sass_0.4.10 yaml_2.3.10
[34] later_1.4.2 pillar_1.10.2 crayon_1.5.3
[37] jquerylib_0.1.4 whisker_0.4.1 cachem_1.1.0
[40] tidyselect_1.2.1 digest_0.6.37 stringi_1.8.7
[43] purrr_1.0.4 dplyr_1.1.4 rprojroot_2.0.4
[46] fastmap_1.2.0 cli_3.6.5 magrittr_2.0.3
[49] withr_3.0.2 filelock_1.0.3 prettyunits_1.2.0
[52] UCSC.utils_1.4.0 promises_1.3.2 rappdirs_0.3.3
[55] bit64_4.6.0-1 rmarkdown_2.29 XVector_0.48.0
[58] httr_1.4.7 bit_4.6.0 png_0.1-8
[61] hms_1.1.3 memoise_2.0.1 evaluate_1.0.3
[64] knitr_1.50 IRanges_2.42.0 BiocFileCache_2.16.1
[67] rlang_1.1.6 Rcpp_1.0.14 glue_1.8.0
[70] DBI_1.2.3 xml2_1.3.8 BiocGenerics_0.54.0
[73] rstudioapi_0.17.1 jsonlite_2.0.0 R6_2.6.1
[76] fs_1.6.6