get_variant: Get Variant

In gtexr: Query the GTEx Portal API

Get Variant

Description

This service returns information about a variant, including position, dbSNP RS ID, the reference allele, the alternative allele, and whether the minor allele frequency is >= 1%. For GTEx v6p, there is also information about whether the whole exome sequence and chip sequencing data are available. Results may be queried by GTEx variant ID (variantId), dbSNP RS ID (snpId) or genomic location (chromosome and pos). Variants are identified based on the genotype data of each dataset cohort, namely, are dataset-dependent. Each variant is assigned a unique GTEx variant ID (i.e. the primary key). Not all variants have a mappable dbSNP RS ID. By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_variant(
  snpId = NULL,
  variantId = NULL,
  chromosome = NULL,
  pos = NULL,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = 250
)

Arguments

snpId	String
variantId	String. A gtex variant ID.
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".
pos	Integer, vector.
datasetId	String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot".
page	Integer (default = 0).
itemsPerPage	Integer (default = 250).

Value

A tibble.

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_functional_annotation(), get_linkage_disequilibrium_by_variant_data(), get_linkage_disequilibrium_data(), get_sample_datasets_endpoints(), get_subject(), get_tissue_site_detail(), get_variant_by_location()

Examples

# search by rsid
get_variant(snpId = "rs1410858")

# search by variantId
get_variant(variantId = "chr1_153209640_C_A_b38")

# search by chromosome and position
get_variant(chromosome = "chr1",
            pos = 153209600:153209700)

gtexr documentation built on Sept. 19, 2024, 5:06 p.m.