calculate_expression_quantitative_trait_loci: Calculate Expression Quantitative Trait Loci

In gtexr: Query the GTEx Portal API

Calculate Expression Quantitative Trait Loci

Description

Calculate your own eQTLs

• This service calculates the gene-variant association for any given pair of gene and variant, which may or may not be significant.

• This requires as input a GENCODE ID, GTEx variant ID, and tissue site detail ID.

By default, the calculation is based on the latest GTEx release.

GTEx Portal API documentation.

Usage

calculate_expression_quantitative_trait_loci(
  tissueSiteDetailId,
  gencodeId,
  variantId,
  datasetId = "gtex_v8"
)

Arguments

tissueSiteDetailId	String. The ID of the tissue of interest. Can be a GTEx specific ID (e.g. "Whole_Blood"; use get_tissue_site_detail() to see valid values) or an Ontology ID.
gencodeId	String. A Versioned GENCODE ID of a gene, e.g. "ENSG00000065613.9".
variantId	String. A gtex variant ID.
datasetId	String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot".

Details

Notes on output:

• Beta and standard error are recorded in columns nes and error respectively (see GTEx FAQs)

• variantId contains (in order) chromosome, position, reference allele, alternative allele and human genome build separated by underscores. The reference and alternative alleles for "chr1_13550_G_A_b38" for example are "G" and "A" respectively.

• See examples for how to calculate minor and alternative allele frequencies.

Notes on input:

• Argument variantId also accepts RSIDs.

Value

A tibble.

See Also

Other Dynamic Association Endpoints: calculate_ieqtls(), calculate_isqtls(), calculate_splicing_quantitative_trait_loci()

Examples

## Not run: 
# perform request - returns a tibble with a single row
calculate_expression_quantitative_trait_loci(tissueSiteDetailId = "Whole_Blood",
                                             gencodeId = "ENSG00000203782.5",
                                             variantId = "rs79641866")

# unnest list columns with tidyr::unnest()
calculate_expression_quantitative_trait_loci(tissueSiteDetailId = "Whole_Blood",
                                             gencodeId = "ENSG00000203782.5",
                                             variantId = "rs79641866") |>
  tidyr::unnest(c("data", "genotypes"))

# to calculate minor and alternative allele frequencies
calculate_expression_quantitative_trait_loci(
  tissueSiteDetailId = "Liver",
  gencodeId = "ENSG00000237973.1",
  variantId = "rs12119111"
) |>
 dplyr::bind_rows(.id = "rsid") |>

 tidyr::separate(
   col = "variantId",
   into = c(
     "chromosome",
     "position",
     "reference_allele",
     "alternative_allele",
     "genome_build"
   ),
   sep = "_"
 ) |>

 # ...then ascertain alternative_allele frequency
 dplyr::mutate(
   alt_allele_count = (2 * homoAltCount) + hetCount,
   total_allele_count = 2 * (homoAltCount + hetCount +  homoRefCount),
   alternative_allele_frequency = alt_allele_count / total_allele_count
 ) |>

 dplyr::select(
   rsid,
   beta = nes,
   se = error,
   pValue,
   minor_allele_frequency = maf,
   alternative_allele_frequency,
   chromosome:genome_build,
   tissueSiteDetailId
 )

## End(Not run)

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