calculate_isqtls: Calculate Isqtls

In gtexr: Query the GTEx Portal API

Calculate Isqtls

Description

Calculate your own Cell Specific sQTLs.

• 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_isqtls(
  cellType,
  tissueSiteDetailId,
  phenotypeId,
  variantId,
  datasetId = "gtex_v8"
)

Arguments

cellType	String. "Adipocytes", "Epithelial_cells", "Hepatocytes", "Keratinocytes", "Myocytes", "Neurons", "Neutrophils".
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.
phenotypeId	String. See GTEx portal FAQs for further details.
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".

Value

A tibble.

See Also

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

Examples

## Not run: 
# perform request
calculate_isqtls(cellType = "Neutrophils",
                 tissueSiteDetailId = "Whole_Blood",
                 phenotypeId = "chr1:15947:16607:clu_40980:ENSG00000227232.5",
                 variantId = "chr1_1099341_T_C_b38")

## End(Not run)

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