Get Gwas Catalog By Location

Find the GWAS Catalog on a certain chromosome between start and end locations.

GTEx API Portal documentation

Usage

get_gwas_catalog_by_location(
  start,
  end,
  chromosome,
  page = 0,
  itemsPerPage = 250
)

Arguments

start

Integer.

end

Integer.

chromosome

String. One of "chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrM", "chrX", "chrY".

page

Integer (default = 0).

itemsPerPage

Integer (default = 250).

Value

A tibble.

See also

Other Reference Genome Endpoints: get_exons(), get_gene_search(), get_genes(), get_genomic_features(), get_neighbor_gene(), get_transcripts()

Examples

# \dontrun{
get_gwas_catalog_by_location(start = 1, end = 10000000, chromosome = "chr1")
#> Warning: ! Total number of items (316) exceeds maximum page size (250).
#> ℹ Try increasing `itemsPerPage`.
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 2
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 316
#> # A tibble: 250 × 10
#>    chromosome   start     end phenotype  pValue   beta pubmedId snpId riskAllele
#>    <chr>        <int>   <int> <chr>       <dbl>  <dbl>    <int> <chr> <chr>     
#>  1 chr1       9653328 9653329 Testicula…  6e-13 1.14   28604728 rs42… T         
#>  2 chr1       8428505 8428506 Autism sp…  7e- 9 1.06   28540026 rs30… ?         
#>  3 chr1       9651584 9651585 Monocyte …  2e- 9 0.0222 27863252 rs75… G         
#>  4 chr1       3080038 3080039 Mean corp…  1e-13 0.0311 27863252 rs15… C         
#>  5 chr1       3811497 3811498 Mean corp…  1e-13 0.0301 27863252 rs12… T         
#>  6 chr1       4544044 4544045 Adolescen…  3e- 9 1.2    26394188 rs24… ?         
#>  7 chr1       1312114 1312115 Inflammat…  8e-13 1.10   23128233 rs12… A         
#>  8 chr1       7961913 7961914 Inflammat…  1e-15 1.11   23128233 rs35… G         
#>  9 chr1       8444361 8444362 Eosinophi…  2e-19 0.0328 27863252 rs15… A         
#> 10 chr1       9281727 9281728 Eosinophi…  1e-10 0.0260 27863252 rs67… T         
#> # ℹ 240 more rows
#> # ℹ 1 more variable: genomeBuild <chr>
# }