Query the Ensembl BioMart web service
Usage
biomart_query(
attrs = NULL,
filters = NULL,
transcript = FALSE,
peptide = FALSE,
gene = FALSE,
dataset = "hsapiens_gene_ensembl"
)Arguments
- attrs
Character vector: one or more Ensembl attribute names.
- filters
Character vector: one or more Ensembl filter names.
- transcript
Logical: include Ensembl transcript IDs in the result.
- peptide
Logical: include Ensembl peptide IDs in the result.
- gene
Logical: include Ensembl gene IDs in the result.
- dataset
Character: An Ensembl dataset name.
Examples
cel_genes <- biomart_query(
attrs = c("external_gene_name", "start_position", "end_position"),
gene = TRUE,
dataset = "celegans_gene_ensembl"
)
cel_genes
#> # A tibble: 46,926 × 4
#> ensembl_gene_id external_gene_name start_position end_position
#> <chr> <chr> <dbl> <dbl>
#> 1 WBGene00000001 aap-1 5107843 5110183
#> 2 WBGene00000002 aat-1 9599178 9601695
#> 3 WBGene00000003 aat-2 9244402 9246360
#> 4 WBGene00000004 aat-3 2552260 2557736
#> 5 WBGene00000005 aat-4 6272529 6275721
#> 6 WBGene00000006 aat-5 2571740 2576020
#> 7 WBGene00000007 aat-6 11466842 11470663
#> 8 WBGene00000008 aat-7 1386870 1391639
#> 9 WBGene00000009 aat-8 3862033 3865044
#> 10 WBGene00000010 aat-9 11388682 11396662
#> # ℹ 46,916 more rows
# # A tibble: 46,934 × 4
# ensembl_gene_id external_gene_name start_position end_position
# <chr> <chr> <dbl> <dbl>
# 1 WBGene00000001 aap-1 5107843 5110183
# 2 WBGene00000002 aat-1 9599178 9601695
# 3 WBGene00000003 aat-2 9244402 9246360
# 4 WBGene00000004 aat-3 2552260 2557736
# 5 WBGene00000005 aat-4 6272529 6275721
# # . with 46,924 more rows