Retrieves variants via the NHGRI-EBI GWAS Catalog REST API. The REST
API is queried multiple times with the criteria passed as arguments (see
below). By default all variants that match the criteria supplied in the
arguments are retrieved: this corresponds to the default option
set_operation set to 'union'. If you rather have only the
variants that match simultaneously all criteria provided, then set
set_operation to 'intersection'.
Usage
get_variants(
study_id = NULL,
association_id = NULL,
variant_id = NULL,
efo_id = NULL,
pubmed_id = NULL,
genomic_range = NULL,
cytogenetic_band = NULL,
gene_name = NULL,
efo_trait = NULL,
reported_trait = NULL,
set_operation = "union",
interactive = TRUE,
std_chromosomes_only = TRUE,
verbose = FALSE,
warnings = TRUE
)Arguments
- study_id
A character vector of GWAS Catalog study accession identifiers.
- association_id
A character vector of GWAS Catalog association identifiers.
- variant_id
A character vector of GWAS Catalog variant identifiers.
- efo_id
A character vector of EFO identifiers.
- pubmed_id
An integer vector of PubMed identifiers.
- genomic_range
A named list of three vectors:
- chromosome
A character vector of chromosome names of the form 1--22, X or Y.
- start
A numeric vector of start positions, starting at 1.
- end
A numeric vector of end positions.
The three vectors need to be of the same length so that
chromosomenames,startandendpositions can be matched by position.- cytogenetic_band
A character vector of cytogenetic bands of the form
'1p36.11'.- gene_name
Gene symbol according to HUGO Gene Nomenclature (HGNC).
- efo_trait
A character vector of EFO trait descriptions, e.g.,
'uric acid measurement'.- reported_trait
A character vector of phenotypic traits as reported by the original authors of the study.
- set_operation
Either
'union'or'intersection'. This tells how variants retrieved by different criteria should be combined:'union'binds together all results removing duplicates and'intersection'only keeps same variants found with different criteria.- interactive
A logical. If all variants are requested, whether to ask interactively if we really want to proceed.
- std_chromosomes_only
Whether to return only variants mapped to standard chromosomes: 1 thru 22, X, Y, and MT.
- verbose
Whether the function should be verbose about the different queries or not.
- warnings
Whether to print warnings.
Value
A variants object.
Details
Please note that all search criteria are vectorised, thus allowing for batch
mode search, e.g., one can search by multiple variant identifiers at once by
passing a vector of identifiers to variant_id.
Examples
# Get variants by study identifier
get_variants(study_id = 'GCST001085', warnings = FALSE)
#> An object of class "variants"
#> Slot "variants":
#> # A tibble: 18 × 7
#> variant_id merged functional_class chromosome_name chromosome_position
#> <chr> <int> <chr> <chr> <int>
#> 1 rs6469823 1 intergenic_variant 8 119341744
#> 2 rs200752 0 intron_variant NA NA
#> 3 rs1372662 0 intron_variant 8 134554803
#> 4 rs2469997 0 intergenic_variant 8 119341027
#> 5 rs12522034 0 intergenic_variant 5 36425491
#> 6 rs7735940 0 regulatory_region_vari… NA NA
#> 7 rs7960483 0 intron_variant NA NA
#> 8 rs6887846 0 intron_variant 5 83140542
#> 9 rs3798440 0 intron_variant NA NA
#> 10 rs6452524 0 intron_variant NA NA
#> 11 rs7827545 0 intron_variant NA NA
#> 12 rs10496288 0 intergenic_variant NA NA
#> 13 rs13420028 0 intron_variant NA NA
#> 14 rs10785581 0 intron_variant 12 45537190
#> 15 rs10188442 0 intron_variant 2 132431666
#> 16 rs10496289 0 intergenic_variant 2 83066256
#> 17 rs9350602 0 intron_variant 6 75850781
#> 18 rs200759 0 intron_variant 20 15625776
#> # ℹ 2 more variables: chromosome_region <chr>, last_update_date <dttm>
#>
#> Slot "genomic_contexts":
#> # A tibble: 60 × 12
#> variant_id gene_name chromosome_name chromosome_position distance
#> <chr> <chr> <chr> <int> <int>
#> 1 rs6469823 CCN3 8 119341744 74702
#> 2 rs6469823 MAL2 8 119341744 96071
#> 3 rs6469823 MIR548AZ 8 119341744 16479
#> 4 rs6469823 MAL2 8 119341744 96071
#> 5 rs6469823 MIR548AZ 8 119341744 16479
#> 6 rs6469823 MAL2-AS1 8 119341744 94887
#> 7 rs6469823 CCN3 8 119341744 74702
#> 8 rs6469823 MAL2-AS1 8 119341744 94896
#> 9 rs1372662 ZFAT 8 134554803 0
#> 10 rs1372662 ZFAT 8 134554803 0
#> # ℹ 50 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: 28 × 3
#> variant_id gene_name ensembl_id
#> <chr> <chr> <chr>
#> 1 rs6469823 CCN3 ENSG00000136999
#> 2 rs6469823 MAL2 ENSG00000147676
#> 3 rs6469823 MIR548AZ ENSG00000276479
#> 4 rs6469823 MAL2-AS1 ENSG00000253972
#> 5 rs1372662 ZFAT ENSG00000066827
#> 6 rs1372662 ZFAT-AS1 ENSG00000248492
#> 7 rs2469997 MAL2 ENSG00000147676
#> 8 rs2469997 MIR548AZ ENSG00000276479
#> 9 rs2469997 CCN3 ENSG00000136999
#> 10 rs2469997 MAL2-AS1 ENSG00000253972
#> # ℹ 18 more rows
#>
#> Slot "entrez_ids":
#> # A tibble: 32 × 3
#> variant_id gene_name entrez_id
#> <chr> <chr> <chr>
#> 1 rs6469823 CCN3 4856
#> 2 rs6469823 MAL2 114569
#> 3 rs6469823 MIR548AZ 102466162
#> 4 rs6469823 MAL2-AS1 105375726
#> 5 rs1372662 ZFAT 57623
#> 6 rs1372662 ZFAT-AS1 594840
#> 7 rs2469997 MAL2 114569
#> 8 rs2469997 MIR548AZ 102466162
#> 9 rs2469997 CCN3 4856
#> 10 rs2469997 MAL2-AS1 105375726
#> # ℹ 22 more rows
#>
# Get a variant by its identifier
if (FALSE) {
get_variants(variant_id = 'rs3798440', warnings = FALSE)
}