Skip to contents

Calculate Isqtls

Source: R/calculate_isqtls.R
calculate_isqtls.Rd

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

# \dontrun{
# perform request
calculate_isqtls(cellType = "Neutrophils",
                 tissueSiteDetailId = "Whole_Blood",
                 phenotypeId = "chr1:15947:16607:clu_40980:ENSG00000227232.5",
                 variantId = "chr1_1099341_T_C_b38")
#> # A tibble: 1 × 9
#>   cellType    data   datasetId enrichmentScores phenotypeId   tissueSiteDetailId
#>   <chr>       <list> <chr>     <list>           <chr>         <chr>             
#> 1 Neutrophils <dbl>  gtex_v8   <dbl [670]>      chr1:15947:1… Whole_Blood       
#> # ℹ 3 more variables: variantId <chr>, genotypes <list>, regressionCoord <list>
# }