ramiromagno
commented
9 months ago This bug is still valid.
library(gwasrapidd)
get_variants(gene_name = "BRCA1")
#> An object of class "variants"
#> Slot "variants":
#> # A tibble: 25 × 7
#> variant_id merged functional_class chromosome_name chromosome_position
#> <chr> <int> <chr> <chr> <int>
#> 1 rs4793187 0 intron_variant 17 42969246
#> 2 rs188757965 0 intron_variant 17 42967552
#> 3 rs80357922 0 frameshift_variant 17 43093535
#> 4 rs55979457 0 intron_variant 17 43017583
#> 5 rs8176229 0 intron_variant 17 43068271
#> 6 rs567534295 0 intron_variant 17 43048090
#> 7 rs535848720 1 intron_variant 17 42969402
#> 8 rs9915489 0 intron_variant 17 43021209
#> 9 rs200576810 0 regulatory_region_var… 17 43014463
#> 10 rs8176071 0 intron_variant 17 43125989
#> # ℹ 15 more rows
#> # ℹ 2 more variables: chromosome_region <chr>, last_update_date <dttm>
#>
#> Slot "genomic_contexts":
#> # A tibble: 652 × 12
#> variant_id gene_name chromosome_name chromosome_position distance
#> <chr> <chr> <chr> <int> <int>
#> 1 rs4793187 RPL27 17 42969246 29027
#> 2 rs4793187 RUNDC1 17 42969246 11319
#> 3 rs4793187 LINC00671 17 42969246 70512
#> 4 rs4793187 PTGES3L 17 42969246 0
#> 5 rs4793187 VAT1 17 42969246 45361
#> 6 rs4793187 AARSD1 17 42969246 4748
#> 7 rs4793187 RUNDC1 17 42969246 11319
#> 8 rs4793187 RPL27 17 42969246 29027
#> 9 rs4793187 RNU6-287P 17 42969246 77811
#> 10 rs4793187 BRCA1 17 42969246 75049
#> # ℹ 642 more rows
#> # ℹ 7 more variables: is_mapped_gene <lgl>, is_closest_gene <lgl>,
#> # is_intergenic <lgl>, is_upstream <lgl>, is_downstream <lgl>, source <chr>,
#> # mapping_method <chr>
#>
#> Slot "ensembl_ids":
#> # A tibble: 257 × 3
#> variant_id gene_name ensembl_id
#> <chr> <chr> <chr>
#> 1 rs4793187 RPL27 ENSG00000131469
#> 2 rs4793187 RUNDC1 ENSG00000198863
#> 3 rs4793187 LINC00671 ENSG00000213373
#> 4 rs4793187 PTGES3L ENSG00000267060
#> 5 rs4793187 VAT1 ENSG00000108828
#> 6 rs4793187 AARSD1 ENSG00000266967
#> 7 rs4793187 RNU6-287P ENSG00000252039
#> 8 rs4793187 BRCA1 ENSG00000012048
#> 9 rs4793187 PTGES3L-AARSD1 ENSG00000108825
#> 10 rs4793187 AOC4P ENSG00000291070
#> # ℹ 247 more rows
#>
#> Slot "entrez_ids":
#> # A tibble: 367 × 3
#> variant_id gene_name entrez_id
#> <chr> <chr> <chr>
#> 1 rs4793187 RPL27 6155
#> 2 rs4793187 RUNDC1 146923
#> 3 rs4793187 LINC00671 388387
#> 4 rs4793187 PTGES3L 100885848
#> 5 rs4793187 VAT1 10493
#> 6 rs4793187 AARSD1 80755
#> 7 rs4793187 RNU6-287P 106481269
#> 8 rs4793187 BRCA1 672
#> 9 rs4793187 PTGES3L-AARSD1 100885850
#> 10 rs4793187 AOC4P 90586
#> # ℹ 357 more rowsCreated on 2023-12-14 with reprex v2.0.2
Check if it still applies: https://rmagno.eu/gwasrapidd/articles/faq.html#5-genomic-coordinates-of-genomic-contexts-seem-to-be-wrong-