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Get Functional Annotation

Source: R/get_functional_annotation.R
get_functional_annotation.Rd

This endpoint retrieves the functional annotation of a certain chromosome location. Default to most recent dataset release.

GTEx Portal API documentation

Usage

get_functional_annotation(
  datasetId = "gtex_v8",
  chromosome,
  start,
  end,
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Arguments

datasetId

String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot".

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".

start

Integer.

end

Integer.

page

Integer (default = 0).

itemsPerPage

Integer (default = 250). Set globally to maximum value 100000 with options(list(gtexr.itemsPerPage = 100000)).

.verbose

Logical. If TRUE (default), print paging information. Set to FALSE globally with options(list(gtexr.verbose = FALSE)).

.return_raw

Logical. If TRUE, return the raw API JSON response. Default = FALSE

Value

A tibble. Or a list if .return_raw = TRUE.

See also

Other Datasets Endpoints: get_annotation(), get_collapsed_gene_model_exon(), get_downloads_page_data(), get_file_list(), get_full_get_collapsed_gene_model_exon(), get_linkage_disequilibrium_by_variant_data(), get_linkage_disequilibrium_data(), get_sample_datasets(), get_subject(), get_tissue_site_detail(), get_variant(), get_variant_by_location()

Examples

get_functional_annotation(chromosome = "chr1", start = 192168000, end = 192169000)
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 3
#> # A tibble: 3 × 23
#>   variantId         enhancer promoter openChromatinRegion promoterFlankingRegion
#>   <chr>             <lgl>    <lgl>    <lgl>               <lgl>                 
#> 1 chr1_192168015_T… TRUE     FALSE    FALSE               FALSE                 
#> 2 chr1_192168266_T… TRUE     FALSE    FALSE               FALSE                 
#> 3 chr1_192168728_T… FALSE    FALSE    FALSE               FALSE                 
#> # ℹ 18 more variables: ctcfBindingSite <lgl>, tfBindingSite <lgl>,
#> #   `3PrimeUtrVariant` <lgl>, `5PrimeUtrVariant` <lgl>,
#> #   frameshiftVariant <lgl>, intronVariant <lgl>, missenseVariant <lgl>,
#> #   nonCodingTranscriptExonVariant <lgl>, spliceAcceptorVariant <lgl>,
#> #   spliceDonorVariant <lgl>, spliceRegionVariant <lgl>, stopGained <lgl>,
#> #   synonymousVariant <lgl>, chromosome <chr>, pos <int>, ref <chr>, alt <chr>,
#> #   datasetId <chr>