gtexr (version 0.2.1)

calculate_isqtls: 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",
  .return_raw = FALSE
)

Value

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

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".

.return_raw

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

See Also

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

Examples

if (FALSE) { # identical(Sys.getenv("IN_PKGDOWN"), "true")
# perform request
calculate_isqtls(
  cellType = "Neutrophils",
  tissueSiteDetailId = "Whole_Blood",
  phenotypeId = "chr1:15947:16607:clu_40980:ENSG00000227232.5",
  variantId = "chr1_1099341_T_C_b38"
)
}