revisit FAQ 5

[ramiromagno]

Check if it still applies:
https://rmagno.eu/gwasrapidd/articles/faq.html#5-genomic-coordinates-of-genomic-contexts-seem-to-be-wrong-

[ramiromagno]

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 rows

^{Created on 2023-12-14 with reprex v2.0.2}