Package 'gtexr'

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

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)

Description

Calculate your own Cell Specific 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_ieqtls(
  cellType,
  tissueSiteDetailId,
  gencodeId,
  variantId,
  datasetId = "gtex_v8"
)

Arguments

Value

A tibble.

See Also

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

Examples

## Not run: 
# perform request
calculate_ieqtls(cellType = "Adipocytes",
                 tissueSiteDetailId = "Adipose_Subcutaneous",
                 gencodeId = "ENSG00000203782.5",
                 variantId = "chr1_1099341_T_C_b38")

## End(Not run)

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

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)

Description

GTEx Portal API documentation.

Usage

calculate_splicing_quantitative_trait_loci(
  tissueSiteDetailId,
  phenotypeId,
  variantId,
  datasetId = "gtex_v8"
)

Arguments

Value

A tibble.

See Also

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

Examples

## Not run: 
# perform request - returns a tibble with a single row
calculate_splicing_quantitative_trait_loci(
  tissueSiteDetailId = "Whole_Blood",
  phenotypeId = "chr1:15947:16607:clu_40980:ENSG00000227232.5",
  variantId = "chr1_14677_G_A_b38")

## End(Not run)

Description

GTEx Portal API documentation

Usage

download(
  materialTypes = NULL,
  tissueSiteDetailIds = NULL,
  pathCategory = NULL,
  tissueSampleIds = NULL,
  sex = NULL,
  sortBy = NULL,
  sortDirection = NULL,
  searchTerm = NULL,
  sampleIds = NULL,
  subjectIds = NULL,
  ageBrackets = NULL,
  hardyScales = NULL,
  hasExpressionData = NULL,
  hasGenotype = NULL
)

Arguments

Details

Note: running this request with no filters (i.e. download()) raises an error.

Value

A tibble

See Also

Other Biobank Data Endpoints: get_sample_biobank_data()

Examples

## Not run: 
download(
  materialTypes = "RNA:Total RNA",
  tissueSiteDetailIds = "Thyroid",
  pathCategory = "clean_specimens",
  sex = "male",
  ageBrackets = "50-59"
)

## End(Not run)

Description

This service returns the list of annotations and allowed values by which a particular dataset can be subsetted. Results may be filtered by dataset.

GTEx Portal API documentation

Usage

get_annotation(datasetId = "gtex_v8", page = 0, itemsPerPage = 250)

Arguments

Details

Note: the output for this function appears to be incomplete currently.

Value

A tibble

See Also

Other Datasets Endpoints: 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(), get_variant_by_location()

Examples

## Not run: 
 get_annotation()

## End(Not run)

Description

Find median transcript expression data along with hierarchical clusters.

• Returns median normalized transcript expression in tissues of all known transcripts of a given gene along with the hierarchical clustering results of tissues and transcripts, based on exon expression, in Newick format.

• The hierarchical clustering is performed by calculating Euclidean distances and using the average linkage method.

• This endpoint is not paginated.

By default, this endpoint queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_clustered_median_exon_expression(
  gencodeIds,
  datasetId = "gtex_v8",
  tissueSiteDetailIds = NULL
)

Arguments

Value

A tibble, with clustering data stored as an attribute, "clusters".

See Also

Other Expression Data Endpoints: get_clustered_median_gene_expression(), get_clustered_median_junction_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), get_gene_expression(), get_median_exon_expression(), get_median_gene_expression(), get_median_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary(), get_top_expressed_genes()

Examples

## Not run: 
get_clustered_median_exon_expression(c("ENSG00000203782.5",
                                       "ENSG00000132693.12"))

# clustering data is stored as an attribute "clusters"
result <- get_clustered_median_exon_expression(c("ENSG00000203782.5",
                                                 "ENSG00000132693.12"))
attr(result, "clusters")

# process clustering data with the ape package
# install.packages("ape")
# phylo_tree <- ape::read.tree(text = attr(result, "clusters")$tissue)
# plot(phylo_tree)
# print(phylo_tree)

## End(Not run)

Description

Find median gene expression data along with hierarchical clusters.

• Returns median gene expression in tissues along with The hierarchical clustering results of tissues and genes, based on gene expression, in Newick format.

• Results may be filtered by dataset, gene or tissue, but at least one gene must be provided

• The hierarchical clustering is performed by calculating Euclidean distances and using the average linkage method.

• This endpoint is not paginated.

By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_clustered_median_gene_expression(
  gencodeIds,
  datasetId = "gtex_v8",
  tissueSiteDetailIds = NULL
)

Arguments

Value

A tibble, with clustering data stored as an attribute, "clusters".

See Also

Other Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_junction_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), get_gene_expression(), get_median_exon_expression(), get_median_gene_expression(), get_median_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary(), get_top_expressed_genes()

Examples

## Not run: 
get_clustered_median_gene_expression(gencodeIds = c("ENSG00000203782.5",
                                                    "ENSG00000132693.12"))

# clustering data is stored as an attribute "clusters"
result <- get_clustered_median_gene_expression(c("ENSG00000203782.5",
                                                 "ENSG00000132693.12"))
attr(result, "clusters")

# process clustering data with the ape package
# install.packages("ape")
# phylo_tree <- ape::read.tree(text = attr(result, "clusters")$tissue)
# plot(phylo_tree)
# print(phylo_tree)

## End(Not run)

Description

Find median junction expression data along with hierarchical clusters.

• Returns median junction read counts in tissues of a given gene from all known transcripts along with the hierarchical clustering results of tissues and genes, based on junction expression, in Newick format.

• Results may be filtered by dataset, gene or tissue, but at least one gene must be provided.

• The hierarchical clustering is performed by calculating Euclidean distances and using the average linkage method.

• This endpoint is not paginated.

By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_clustered_median_junction_expression(
  gencodeIds,
  datasetId = "gtex_v8",
  tissueSiteDetailIds = NULL
)

Arguments

Value

A tibble, with clustering data stored as an attribute, "clusters".

See Also

Other Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_gene_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), get_gene_expression(), get_median_exon_expression(), get_median_gene_expression(), get_median_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary(), get_top_expressed_genes()

Examples

## Not run: 
get_clustered_median_junction_expression(gencodeIds = c("ENSG00000203782.5",
                                                    "ENSG00000132693.12"))

# clustering data is stored as an attribute "clusters"
result <- get_clustered_median_junction_expression(c("ENSG00000203782.5",
                                                 "ENSG00000132693.12"))
attr(result, "clusters")

# process clustering data with the ape package
# install.packages("ape")
# phylo_tree <- ape::read.tree(text = attr(result, "clusters")$tissue)
# plot(phylo_tree)
# print(phylo_tree)

## End(Not run)

Description

Find median transcript expression data of all known transcripts of a gene along with hierarchical clusters.

• Returns median normalized expression in tissues of all known transcripts of a given gene along with the hierarchical clustering results of tissues and genes, based on expression, in Newick format.

• Results may be filtered by dataset, gene or tissue, but at least one gene must be provided.

• The hierarchical clustering is performed by calculating Euclidean distances and using the average linkage method.

• This endpoint is not paginated.

By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_clustered_median_transcript_expression(
  gencodeIds,
  datasetId = "gtex_v8",
  tissueSiteDetailIds = NULL
)

Arguments

Value

A tibble, with clustering data stored as an attribute, "clusters".

See Also

Other Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_gene_expression(), get_clustered_median_junction_expression(), get_expression_pca(), get_gene_expression(), get_median_exon_expression(), get_median_gene_expression(), get_median_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary(), get_top_expressed_genes()

Examples

## Not run: 
get_clustered_median_transcript_expression(gencodeIds = c("ENSG00000203782.5",
                                                    "ENSG00000132693.12"))

# clustering data is stored as an attribute "clusters"
result <- get_clustered_median_transcript_expression(c("ENSG00000203782.5",
                                                 "ENSG00000132693.12"))
attr(result, "clusters")

# process clustering data with the ape package
# install.packages("ape")
# phylo_tree <- ape::read.tree(text = attr(result, "clusters")$tissue)
# plot(phylo_tree)
# print(phylo_tree)

## End(Not run)

Description

This service returns the collapsed exons in the gene model of the given gene. Gene-level and exon-level expression quantification were based on the GENCODE annotation, collapsed to a single transcript model for each gene using an algorithm developed by the GTEx analysis team.

By default, this service queries the models used by the latest GTEx release.

GTEx Portal API documentation

Usage

get_collapsed_gene_model_exon(
  gencodeId,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble

See Also

Other Datasets Endpoints: get_annotation(), 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(), get_variant_by_location()

Examples

## Not run: 
 get_collapsed_gene_model_exon(gencodeId = "ENSG00000132693.12")

## End(Not run)

Description

GTEx Portal API documentation

Usage

get_dataset_info(datasetId = "gtex_v8", organizationName = "GTEx Consortium")

Arguments

Details

Note: this current only returns empty values.

Value

A tibble.

Examples

## Not run: 
get_dataset_info()

## End(Not run)

Description

Retrieves all the files belonging to the given project_id for display on the ⁠Downloads Page⁠

GTEx Portal API documentation

Usage

get_downloads_page_data(project_id = "adult-gtex")

Arguments

Details

Note: The GTEx Portal API documentation states "GTEx currently has one project available: gtex". However, project_id values "adult-gtex" and "egtex" both return results, whereas "gtex" does not (see examples).

Value

A Tibble

See Also

Other Datasets Endpoints: get_annotation(), get_collapsed_gene_model_exon(), 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(), get_variant_by_location()

Examples

## Not run: 
 # "adult-gtex" (default `project_id` value) and "egtex" both return results
 get_downloads_page_data()
 egtex <- get_downloads_page_data("egtex")
 egtex

 # ..."gtex" does not
 get_downloads_page_data("gtex")

 # get details for whole blood methylation data, including download URL
 purrr::pluck(
   egtex$children,
   1,
   "folders",
   "Methylation - EPIC Array",
   "children",
   "folders",
   "mQTLs",
   "children",
   "files",
   "WholeBlood.mQTLs.regular.txt.gz"
 )

## End(Not run)

Description

Retrieve eGenes (eQTL Genes).

• This service returns eGenes (eQTL Genes) from the specified dataset.

• eGenes are genes that have at least one significant cis-eQTL acting upon them.

• Results may be filtered by tissue. By default, the service queries the latest GTEx release.

For each eGene, the results include the allelic fold change (log2AllelicFoldChange), p-value (pValue), p-value threshold (pValueThreshold), empirical p-value (empiricalPValue), and q-value (qValue).

• The log2AllelicFoldChange is the allelic fold change (in log2 scale) of the most significant eQTL.

• The pValue is the nominal p-value of the most significant eQTL.

• The pValueThreshold is the p-value threshold used to determine whether a cis-eQTL for this gene is significant. For more details see https://gtexportal.org/home/documentationPage#staticTextAnalysisMethods.

• The empiricalPValue is the beta distribution-adjusted empirical p-value from FastQTL.

• The qValues were calculated based on the empirical p-values. A false discovery rate (FDR) threshold of <= 0.05 was applied to identify genes with a significant eQTL.

GTEx Portal API documentation.

Usage

get_eqtl_genes(
  tissueSiteDetailIds,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Static Association Endpoints: get_fine_mapping(), get_independent_eqtl(), get_multi_tissue_eqtls(), get_significant_single_tissue_eqtls(), get_significant_single_tissue_eqtls_by_location(), get_significant_single_tissue_ieqtls(), get_significant_single_tissue_isqtls(), get_significant_single_tissue_sqtls(), get_sqtl_genes()

Examples

## Not run: 
get_eqtl_genes(c("Whole_Blood", "Artery_Aorta"))

## End(Not run)

Description

This service returns exons from all known transcripts of the given gene.

• A versioned GENCODE ID is required to ensure that all exons are from a single gene.

• A dataset ID or both GENCODE version and genome build must be provided.

• Although annotated exons are not dataset dependent, specifying a dataset here is equivalent to specifying the GENCODE version and genome build used by that dataset.

GTEx Portal API documentation

Usage

get_exons(
  gencodeId,
  gencodeVersion = NULL,
  genomeBuild = NULL,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Reference Genome Endpoints: get_gene_search(), get_genes(), get_genomic_features(), get_gwas_catalog_by_location(), get_neighbor_gene(), get_transcripts()

Examples

## Not run: 
get_exons(gencodeId = "ENSG00000203782.5")

## End(Not run)

Description

Find gene expression PCA data.

• Returns gene expression PCA (principal component analysis) in tissues.

• Results may be filtered by tissue, sample, or dataset.

By default, the service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_expression_pca(
  tissueSiteDetailIds,
  datasetId = "gtex_v8",
  sampleId = NULL,
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_gene_expression(), get_clustered_median_junction_expression(), get_clustered_median_transcript_expression(), get_gene_expression(), get_median_exon_expression(), get_median_gene_expression(), get_median_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary(), get_top_expressed_genes()

Examples

## Not run: 
get_expression_pca(tissueSiteDetailIds = c("Adipose_Subcutaneous",
                                           "Whole_Blood"))

get_expression_pca(tissueSiteDetailIds = "Adipose_Subcutaneous",
                   sampleId = "GTEX-1117F-0226-SM-5GZZ7")

## End(Not run)

Description

Get all the files in GTEx dataset for Download page

GTEx Portal API documentation

Usage

get_file_list()

Details

The returned tibble includes a nested list column, "filesets". This details files, sub-categorised by fileset (see examples section).

Value

A tibble

See Also

Other Datasets Endpoints: get_annotation(), get_collapsed_gene_model_exon(), get_downloads_page_data(), 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(), get_variant_by_location()

Examples

## Not run: 
# Column "filesets" is a list column
get_file_list()

# Get "GTEx Analysis V9" file list
gtex_v9_files <- get_file_list() |>
                   dplyr::filter(name == "GTEx Analysis V9") |>
                   dplyr::pull(filesets)

# "GTEx Analysis V9" filesets
names(gtex_v9_files[[1]])

# "GTEx Analysis V9", "snRNA-Seq Data" fileset files
names(gtex_v9_files[[1]][["snRNA-Seq Data"]]$files)

## End(Not run)

Description

Retrieve Fine Mapping Data

• Finds and returns ⁠Fine Mapping⁠ data for the provided list of genes

• By default, this endpoint fetches data from the latest GTEx version

The retrieved data is split into pages with items_per_page entries per page

GTEx Portal API documentation

Usage

get_fine_mapping(
  gencodeIds,
  datasetId = "gtex_v8",
  variantId = NULL,
  tissueSiteDetailIds = NULL,
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Static Association Endpoints: get_eqtl_genes(), get_independent_eqtl(), get_multi_tissue_eqtls(), get_significant_single_tissue_eqtls(), get_significant_single_tissue_eqtls_by_location(), get_significant_single_tissue_ieqtls(), get_significant_single_tissue_isqtls(), get_significant_single_tissue_sqtls(), get_sqtl_genes()

Examples

## Not run: 
# search by gene
get_fine_mapping(gencodeIds = c("ENSG00000132693.12",
                               "ENSG00000203782.5"))

# optionally filter for a single variant and/or one or more tissues
get_fine_mapping(gencodeIds = c("ENSG00000132693.12",
                               "ENSG00000203782.5"),
                 variantId = "chr1_153228363_A_G_b38",
                 tissueSiteDetailIds = c("Whole_Blood",
                                        "Thyroid"))

## End(Not run)

Description

This service allows the user to query the full Collapsed Gene Model Exon of a specific gene by gencode ID

GTEx Portal API documentation

Usage

get_full_get_collapsed_gene_model_exon(gencodeId, page = 0, itemsPerPage = 250)

Arguments

Value

A tibble

See Also

Other Datasets Endpoints: get_annotation(), get_collapsed_gene_model_exon(), get_downloads_page_data(), get_file_list(), 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(), get_variant_by_location()

Examples

## Not run: 
  get_full_get_collapsed_gene_model_exon(gencodeId = "ENSG00000203782.5")

## End(Not run)

Description

This endpoint retrieves the functional annotation of a certain chromosome location. Default to most recent dataset release.

GTEx Portal API documentation

Usage

get_functional_annotation(
  datasetId = "gtex_v8",
  chromosome,
  start,
  end,
  page = 0,
  itemsPerPage = 250
)

Arguments

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_linkage_disequilibrium_by_variant_data(), get_linkage_disequilibrium_data(), get_sample_datasets_endpoints(), get_subject(), get_tissue_site_detail(), get_variant(), get_variant_by_location()

Examples

## Not run: 
  get_functional_annotation(chromosome = "chr1", start = 192168000, end = 192169000)

## End(Not run)

Description

Find normalized gene expression data.

• Returns normalized gene expression in tissues at the sample level.

• Results may be filtered by dataset, gene or tissue, but at least one gene must be provided.

By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_gene_expression(
  gencodeIds,
  datasetId = "gtex_v8",
  tissueSiteDetailIds = NULL,
  attributeSubset = NULL,
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_gene_expression(), get_clustered_median_junction_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), get_median_exon_expression(), get_median_gene_expression(), get_median_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary(), get_top_expressed_genes()

Examples

## Not run: 
  # multiple genes, selected tissues
  get_gene_expression(gencodeIds = c("ENSG00000132693.12",
                                     "ENSG00000203782.5"),
                      tissueSiteDetailIds = c("Thyroid", "Whole_Blood"))

  # single gene, selected (single) tissue
  get_gene_expression(gencodeIds = "ENSG00000132693.12",
                      tissueSiteDetailIds = "Whole_Blood")

  # subset by sex
  get_gene_expression(gencodeIds = "ENSG00000132693.12",
                      tissueSiteDetailIds = "Whole_Blood",
                      attributeSubset = "sex")

  # subset by age bracket
  get_gene_expression(gencodeIds = "ENSG00000132693.12",
                      tissueSiteDetailIds = "Whole_Blood",
                      attributeSubset = "ageBracket")

## End(Not run)

Description

Find genes that are partial or complete match of a gene_id

• gene_id could be a gene symbol, a gencode ID, or an Ensemble ID

• Gencode Version and Genome Build must be specified

GTEx Portal API documentation

Usage

get_gene_search(
  geneId,
  gencodeVersion = "v26",
  genomeBuild = "GRCh38/hg38",
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Reference Genome Endpoints: get_exons(), get_genes(), get_genomic_features(), get_gwas_catalog_by_location(), get_neighbor_gene(), get_transcripts()

Examples

## Not run: 
get_gene_search("CRP")

## End(Not run)

Description

This service returns information about reference genes. A genome build and GENCODE version must be provided.

• Genes are searchable by gene symbol, GENCODE ID and versioned GENCODE ID.

• Versioned GENCODE ID is recommended to ensure unique ID matching.

• By default, this service queries the genome build and GENCODE version used by the latest GTEx release.

GTEx API Portal documentation

Usage

get_genes(
  geneIds,
  gencodeVersion = "v26",
  genomeBuild = "GRCh38/hg38",
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble

See Also

Other Reference Genome Endpoints: get_exons(), get_gene_search(), get_genomic_features(), get_gwas_catalog_by_location(), get_neighbor_gene(), get_transcripts()

Examples

## Not run: 
get_genes(c("CRP", "IL6R"))

## End(Not run)

Description

GTEx API Portal documentation

Usage

get_genomic_features(.featureId, datasetId = "gtex_v8")

Arguments

Details

This endpoint takes a path parameter "featureId".

Value

A tibble.

See Also

Other Reference Genome Endpoints: get_exons(), get_gene_search(), get_genes(), get_gwas_catalog_by_location(), get_neighbor_gene(), get_transcripts()

Examples

## Not run: 
# gene symbol
get_genomic_features("brca1")

# GENCODE ID
get_genomic_features("ENSG00000132693.12")

# RSID
get_genomic_features("rs1815739")

# GTEx variant ID
get_genomic_features("chr11_66561023_G_GTTA_b38")

## End(Not run)

Description

Find the GWAS Catalog on a certain chromosome between start and end locations.

GTEx API Portal documentation

Usage

get_gwas_catalog_by_location(
  start,
  end,
  chromosome,
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Reference Genome Endpoints: get_exons(), get_gene_search(), get_genes(), get_genomic_features(), get_neighbor_gene(), get_transcripts()

Examples

## Not run: 
get_gwas_catalog_by_location(start = 1, end = 10000000, chromosome = "chr1")

## End(Not run)

Description

GTEx Portal API documentation

Usage

get_image(tissueSampleIds = NULL, page = 0, itemsPerPage = 250)

Arguments

Value

A tibble.

Examples

## Not run: 
get_image()

# filter by `tissueSampleId`
result <- get_image(tissueSampleIds = "GTEX-1117F-0526")
print(result)

# note that `pathologyNotesCategories` (if present) is a list column
print(result$pathologyNotesCategories)

## End(Not run)

Description

Retrieve Independent eQTL Data

• Finds and returns ⁠Independent eQTL Data⁠ data for the provided list of genes

• By default, this endpoint fetches data from the latest GTEx version

The retrieved data is split into pages with items_per_page entries per page

GTEx portal API documentation

Usage

get_independent_eqtl(
  gencodeIds,
  tissueSiteDetailIds = NULL,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Static Association Endpoints: get_eqtl_genes(), get_fine_mapping(), get_multi_tissue_eqtls(), get_significant_single_tissue_eqtls(), get_significant_single_tissue_eqtls_by_location(), get_significant_single_tissue_ieqtls(), get_significant_single_tissue_isqtls(), get_significant_single_tissue_sqtls(), get_sqtl_genes()

Examples

## Not run: 
# search by gene
get_independent_eqtl(gencodeIds = c("ENSG00000132693.12",
                               "ENSG00000203782.5"))

# optionally filter for a single variant and/or one or more tissues
get_independent_eqtl(gencodeIds = c("ENSG00000132693.12",
                                    "ENSG00000203782.5"),
                     tissueSiteDetailIds = c("Whole_Blood",
                                             "Thyroid"))

## End(Not run)

Description

Find linkage disequilibrium (LD) data for a given variant

GTEx Portal API documentation

Usage

get_linkage_disequilibrium_by_variant_data(
  variantId,
  page = 0,
  itemsPerPage = 250
)

Arguments

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_data(), get_sample_datasets_endpoints(), get_subject(), get_tissue_site_detail(), get_variant(), get_variant_by_location()

Examples

get_linkage_disequilibrium_by_variant_data("chr1_159245536_C_T_b38")

Description

Find linkage disequilibrium (LD) data for a given gene.

This endpoint returns linkage disequilibrium data for the cis-eQTLs found associated with the provided gene in a specified dataset. Results are queried by gencode ID. By default, the service queries the latest GTEx release. Specify a dataset ID to fetch results from a different dataset.

GTEx Portal API documentation

Usage

get_linkage_disequilibrium_data(
  gencodeId,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = 250
)

Arguments

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_sample_datasets_endpoints(), get_subject(), get_tissue_site_detail(), get_variant(), get_variant_by_location()

Examples

get_linkage_disequilibrium_data(gencodeId = "ENSG00000132693.12")

Description

Getting all the maintenance messages from the database that are enabled.

GTEx Portal API documentation.

Usage

get_maintenance_message(page = 0, itemsPerPage = 250)

Arguments

Details

Note this typically returns an empty tibble.

Value

A tibble.

See Also

Other Admin Endpoints: get_news_item()

Examples

## Not run: 
get_maintenance_message()

## End(Not run)

Description

Find median exon expression data.

• Returns median exon read counts, in tissues, of a collapsed gene model.

• Results may be filtered by dataset, gene or tissue, but at least one gene must be provided

By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_median_exon_expression(
  gencodeIds,
  datasetId = "gtex_v8",
  tissueSiteDetailIds = NULL,
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_gene_expression(), get_clustered_median_junction_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), get_gene_expression(), get_median_gene_expression(), get_median_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary(), get_top_expressed_genes()

Examples

## Not run: 
# median exon expression values for CRP, filtered for whole blood
get_median_exon_expression(gencodeIds = "ENSG00000132693.12",
                           tissueSiteDetailIds = "Whole_Blood")

## End(Not run)

Description

Find median gene expression data along with hierarchical clusters.

• Returns median gene expression in tissues.

• By default, this endpoint queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_median_gene_expression(
  gencodeIds,
  datasetId = "gtex_v8",
  tissueSiteDetailIds = NULL,
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_gene_expression(), get_clustered_median_junction_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), get_gene_expression(), get_median_exon_expression(), get_median_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary(), get_top_expressed_genes()

Examples

## Not run: 
get_median_gene_expression(gencodeIds = "ENSG00000132693.12")

## End(Not run)

Description

Find junction gene expression data.

• Returns median junction read counts in tissues of a given gene from all known transcripts.

• Results may be filtered by dataset or tissue.

By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_median_junction_expression(
  gencodeIds,
  datasetId = "gtex_v8",
  tissueSiteDetailIds = NULL,
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_gene_expression(), get_clustered_median_junction_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), get_gene_expression(), get_median_exon_expression(), get_median_gene_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary(), get_top_expressed_genes()

Examples

## Not run: 
get_median_junction_expression(gencodeIds = "ENSG00000132693.12")

## End(Not run)

Description

Find median transcript expression data of all known transcripts of a gene.

• Returns median normalized expression in tissues of all known transcripts of a given gene.

• Results may be filtered by dataset or tissue.

By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_median_transcript_expression(
  gencodeIds,
  datasetId = "gtex_v8",
  tissueSiteDetailIds = NULL,
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_gene_expression(), get_clustered_median_junction_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), get_gene_expression(), get_median_exon_expression(), get_median_gene_expression(), get_median_junction_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary(), get_top_expressed_genes()

Examples

## Not run: 
get_median_transcript_expression(gencodeIds = "ENSG00000132693.12")

## End(Not run)

Description

Find multi-tissue eQTL Metasoft results.

• This service returns multi-tissue eQTL Metasoft results for a given gene and variant in a specified dataset.

• A Versioned GENCODE ID must be provided.

• For each tissue, the results include: m-value (mValue), normalized effect size (nes), p-value (pValue), and standard error (se).

• The m-value is the posterior probability that an eQTL effect exists in each tissue tested in the cross-tissue meta-analysis (Han and Eskin, PLoS Genetics 8(3): e1002555, 2012).

• The normalized effect size is the slope of the linear regression of normalized expression data versus the three genotype categories using single-tissue eQTL analysis, representing eQTL effect size.

• The p-value is from a t-test that compares observed NES from single-tissue eQTL analysis to a null NES of 0.

By default, the service queries the latest GTEx release. The retrieved data is split into pages with items_per_page entries per page

GTEx Portal API documentation

Usage

get_multi_tissue_eqtls(
  gencodeIds,
  variantId = NULL,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Static Association Endpoints: get_eqtl_genes(), get_fine_mapping(), get_independent_eqtl(), get_significant_single_tissue_eqtls(), get_significant_single_tissue_eqtls_by_location(), get_significant_single_tissue_ieqtls(), get_significant_single_tissue_isqtls(), get_significant_single_tissue_sqtls(), get_sqtl_genes()

Examples

## Not run: 
# search by gene
get_multi_tissue_eqtls(gencodeId = c("ENSG00000132693.12",
                                     "ENSG00000203782.5"))

## End(Not run)

Description

Find all neighboring genes on a certain chromosome around a position with a certain window size.

GTEx API Portal documentation

Usage

get_neighbor_gene(pos, chromosome, bp_window, page = 0, itemsPerPage = 250)

Arguments

Value

A tibble.

See Also

Other Reference Genome Endpoints: get_exons(), get_gene_search(), get_genes(), get_genomic_features(), get_gwas_catalog_by_location(), get_transcripts()

Examples

## Not run: 
get_neighbor_gene(pos = 1000000, chromosome = "chr1", bp_window = 10000)

## End(Not run)

Description

Getting all the news items from the database that are current.

GTEx Portal API documentation.

Usage

get_news_item(page = 0, itemsPerPage = 250)

Arguments

Value

A tibble.

See Also

Other Admin Endpoints: get_maintenance_message()

Examples

## Not run: 
get_news_item()

## End(Not run)

Description

GTEx Portal API documentation

Usage

get_sample_biobank_data(
  draw = NULL,
  materialTypes = NULL,
  tissueSiteDetailIds = NULL,
  pathCategory = NULL,
  tissueSampleIds = NULL,
  sex = NULL,
  sortBy = "sampleId",
  sortDirection = "asc",
  searchTerm = NULL,
  sampleIds = NULL,
  subjectIds = NULL,
  ageBrackets = NULL,
  hardyScales = NULL,
  hasExpressionData = NULL,
  hasGenotype = NULL,
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble

See Also

Other Biobank Data Endpoints: download()

Examples

## Not run: 
 get_sample_biobank_data(tissueSiteDetailIds = "Whole_Blood")

## End(Not run)

Description

This service returns information of samples used in analyses from all datasets. Results may be filtered by dataset ID, sample ID, subject ID, sample metadata, or other provided parameters. By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_sample_datasets_endpoints(
  datasetId = "gtex_v8",
  sampleIds = NULL,
  tissueSampleIds = NULL,
  subjectIds = NULL,
  ageBrackets = NULL,
  sex = NULL,
  pathCategory = NULL,
  tissueSiteDetailId = NULL,
  aliquotIds = NULL,
  autolysisScores = NULL,
  hardyScales = NULL,
  ischemicTime = NULL,
  ischemicTimeGroups = NULL,
  rin = NULL,
  uberonIds = NULL,
  dataTypes = NULL,
  sortBy = NULL,
  sortDirection = NULL,
  page = NULL,
  itemsPerPage = NULL
)

Arguments

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_subject(), get_tissue_site_detail(), get_variant(), get_variant_by_location()

Examples

## Not run: 
 get_sample_datasets_endpoints()

## End(Not run)

Description

General information about the GTEx service.

GTEx Portal API documentation.

Usage

get_service_info()

Value

A tibble.

Examples

## Not run: 
get_service_info()

## End(Not run)

Description

Find significant single tissue eQTLs.

• This service returns precomputed significant single tissue eQTLs.

• Results may be filtered by tissue, gene, variant or dataset.

• To search by gene, use the versioned GENCODE ID.

• To search by variant, use the dbSNP rs ID (snpId).

By default, the service queries the latest GTEx release and the retrieved data is split into pages with items_per_page entries per page

GTEx Portal API documentation.

Usage

get_significant_single_tissue_eqtls(
  gencodeIds = NULL,
  variantIds = NULL,
  tissueSiteDetailIds = NULL,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = 250
)

Arguments

Details

Note: although the GTEx Portal API documentation says to use the dbSNP rsID when searching by variant, this returns no results. Instead use gtex variant IDs e.g. use "chr1_153209640_C_A_b38" instead of "rs1410858".

Value

A tibble.

See Also

Other Static Association Endpoints: get_eqtl_genes(), get_fine_mapping(), get_independent_eqtl(), get_multi_tissue_eqtls(), get_significant_single_tissue_eqtls_by_location(), get_significant_single_tissue_ieqtls(), get_significant_single_tissue_isqtls(), get_significant_single_tissue_sqtls(), get_sqtl_genes()

Examples

## Not run: 
# search by gene
get_significant_single_tissue_eqtls(gencodeIds = c("ENSG00000132693.12",
                                                  "ENSG00000203782.5"))

# search by variant - must be variantId (not rsid)
get_significant_single_tissue_eqtls(variantIds = "chr1_153209640_C_A_b38")

# filter by gene/variant and tissue site - either `gencodeIds` or `variantIds`
# should be supplied as a minimum
get_significant_single_tissue_eqtls(gencodeIds = c("ENSG00000132693.12",
                                                  "ENSG00000203782.5"),
                                    variantIds = "chr1_153209640_C_A_b38",
                                    tissueSiteDetailIds = "Whole_Blood")

## End(Not run)

Description

Find significant single tissue eQTLs using Chromosomal Locations.

• This service returns precomputed significant single tissue eQTLs.

• Results may be filtered by tissue, and/or dataset.

By default, the service queries the latest GTEx release. Since this endpoint is used to support a third party program on the portal, the return structure is different from other endpoints and is not paginated.

GTEx Portal API documentation

Usage

get_significant_single_tissue_eqtls_by_location(
  tissueSiteDetailId,
  start,
  end,
  chromosome,
  datasetId = "gtex_v8"
)

Arguments

Value

A tibble.

See Also

Other Static Association Endpoints: get_eqtl_genes(), get_fine_mapping(), get_independent_eqtl(), get_multi_tissue_eqtls(), get_significant_single_tissue_eqtls(), get_significant_single_tissue_ieqtls(), get_significant_single_tissue_isqtls(), get_significant_single_tissue_sqtls(), get_sqtl_genes()

Examples

## Not run: 
get_significant_single_tissue_eqtls_by_location(
  tissueSiteDetailId = "Artery_Aorta",
  start = 10000,
  end = 250000,
  chromosome = "chr11")

## End(Not run)

Description

Retrieve Interaction eQTL Data.

• This service returns cell type interaction eQTLs (ieQTLs), from a specified dataset.

• Results may be filtered by tissue

• By default, the service queries the latest GTEx release.

The retrieved data is split into pages with items_per_page entries per page

GTEx Portal API documentation

Usage

get_significant_single_tissue_ieqtls(
  gencodeIds,
  variantIds = NULL,
  tissueSiteDetailIds = NULL,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble

See Also

Other Static Association Endpoints: get_eqtl_genes(), get_fine_mapping(), get_independent_eqtl(), get_multi_tissue_eqtls(), get_significant_single_tissue_eqtls(), get_significant_single_tissue_eqtls_by_location(), get_significant_single_tissue_isqtls(), get_significant_single_tissue_sqtls(), get_sqtl_genes()

Examples

## Not run: 
get_significant_single_tissue_ieqtls(c("ENSG00000132693.12",
                                       "ENSG00000203782.5"))

## End(Not run)

Description

Retrieve Interaction sQTL Data.

• This service retrieves cell type interaction sQTLs (isQTLs), from a specified dataset.

• Results may be filtered by tissue

• By default, the service queries the latest GTEx release.

The retrieved data is split into pages with items_per_page entries per page

GTEx Portal API documentation.

Usage

get_significant_single_tissue_isqtls(
  gencodeIds,
  variantIds = NULL,
  tissueSiteDetailIds = NULL,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble

See Also

Other Static Association Endpoints: get_eqtl_genes(), get_fine_mapping(), get_independent_eqtl(), get_multi_tissue_eqtls(), get_significant_single_tissue_eqtls(), get_significant_single_tissue_eqtls_by_location(), get_significant_single_tissue_ieqtls(), get_significant_single_tissue_sqtls(), get_sqtl_genes()

Examples

## Not run: 
get_significant_single_tissue_isqtls(gencodeIds = c("ENSG00000065613.9",
                                                    "ENSG00000203782.5"))

## End(Not run)

Description

Retrieve Single Tissue sQTL Data.

• This service returns single tissue sQTL data for the given genes, from a specified dataset.

• Results may be filtered by tissue

• By default, the service queries the latest GTEx release.

The retrieved data is split into pages with items_per_page entries per page

GTEx Portal API documentation.

Usage

get_significant_single_tissue_sqtls(
  gencodeIds,
  variantIds = NULL,
  tissueSiteDetailIds = NULL,
  datasetId = "gtex_v8"
)

Arguments

Value

A tibble

See Also

Other Static Association Endpoints: get_eqtl_genes(), get_fine_mapping(), get_independent_eqtl(), get_multi_tissue_eqtls(), get_significant_single_tissue_eqtls(), get_significant_single_tissue_eqtls_by_location(), get_significant_single_tissue_ieqtls(), get_significant_single_tissue_isqtls(), get_sqtl_genes()

Examples

## Not run: 
# search by gene
get_significant_single_tissue_sqtls(gencodeIds = c("ENSG00000065613.9",
                                                   "ENSG00000203782.5"))

## End(Not run)

Description

Retrieve Single Nucleus Gene Expression Data for a given Gene.

GTEx Portal API documentation

Usage

get_single_nucleus_gex(
  gencodeIds,
  datasetId = "gtex_snrnaseq_pilot",
  tissueSiteDetailIds = NULL,
  excludeDataArray = TRUE,
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble

See Also

Other Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_gene_expression(), get_clustered_median_junction_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), get_gene_expression(), get_median_exon_expression(), get_median_gene_expression(), get_median_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex_summary(), get_top_expressed_genes()

Examples

## Not run: 
# Search for one or more genes - returns a tibble with one row per tissue.
# Column "cellTypes" now contains a tibble of expression summary data, with
# one row for each cell type
get_single_nucleus_gex(gencodeIds = c("ENSG00000203782.5",
                                      "ENSG00000132693.12"))

# `excludeDataArray = FALSE` - expression values are stored under "celltypes"
# in an additional column called "data"
response <- get_single_nucleus_gex(gencodeIds = "ENSG00000132693.12",
                                   excludeDataArray = FALSE,
                                   itemsPerPage = 2)

response

# "cellTypes" contains a tibble of data with one row for each
# cell type e.g. for Breast_Mammary_Tissue
response$cellTypes[[2]]

# when `excludeDataArray = FALSE`, expression values are stored in "data"
# e.g. for Breast_Mammary_Tissue, Epithelial cell (luminal):
response$cellTypes[[2]]$data[[1]]

## End(Not run)

Description

Retrieve Summarized Single Nucleus Gene Expression Data.

GTEx Portal API documentation

Usage

get_single_nucleus_gex_summary(
  datasetId = "gtex_snrnaseq_pilot",
  tissueSiteDetailIds = NULL,
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_gene_expression(), get_clustered_median_junction_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), get_gene_expression(), get_median_exon_expression(), get_median_gene_expression(), get_median_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_top_expressed_genes()

Examples

## Not run: 
# all tissues
get_single_nucleus_gex_summary()

# filter for specific tissue
get_single_nucleus_gex_summary(tissueSiteDetailIds = c("Breast_Mammary_Tissue",
                                                       "Skin_Sun_Exposed_Lower_leg"))

## End(Not run)

Description

Retrieve sGenes (sQTL Genes).

• This service returns sGenes (sQTL Genes) from the specified dataset.

• Results may be filtered by tissue.

• By default, the service queries the latest GTEx release.

The retrieved data is split into pages with items_per_page entries per page

GTEx Portal API documentation.

Usage

get_sqtl_genes(
  tissueSiteDetailId,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Static Association Endpoints: get_eqtl_genes(), get_fine_mapping(), get_independent_eqtl(), get_multi_tissue_eqtls(), get_significant_single_tissue_eqtls(), get_significant_single_tissue_eqtls_by_location(), get_significant_single_tissue_ieqtls(), get_significant_single_tissue_isqtls(), get_significant_single_tissue_sqtls()

Examples

## Not run: 
get_sqtl_genes("Whole_Blood")

## End(Not run)

Description

This service returns information of subjects used in analyses from all datasets. Results may be filtered by dataset ID, subject ID, sex, age bracket or Hardy Scale. By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_subject(
  datasetId = "gtex_v8",
  sex = NULL,
  ageBrackets = NULL,
  hardyScales = NULL,
  subjectIds = NULL,
  page = 0,
  itemsPerPage = 250
)

Arguments

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_tissue_site_detail(), get_variant(), get_variant_by_location()

Examples

## Not run: 
  get_subject()

## End(Not run)

Description

Retrieve all tissue site detail information in the database

GTEx Portal API documentation

Usage

get_tissue_site_detail(page = 0, itemsPerPage = 250)

Arguments

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_variant(), get_variant_by_location()

Examples

## Not run: 
  # returns a tibble with one row per tissue
  get_tissue_site_detail()

  # `eqtlSampleSummary` and `rnaSeqSampleSummary` are list columns
  bladder_site_details <- get_tissue_site_detail() |>
    dplyr::filter(tissueSiteDetailId == "Bladder")

  purrr::pluck(bladder_site_details, "eqtlSampleSummary", 1)

  purrr::pluck(bladder_site_details, "rnaSeqSampleSummary", 1)

## End(Not run)

Description

Find top expressed genes for a specified tissue.

• Returns top expressed genes for a specified tissue in a dataset, sorted by median expression.

• When the optional parameter filterMtGene is set to true, mitochondrial genes will be excluded from the results. By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_top_expressed_genes(
  tissueSiteDetailId,
  datasetId = "gtex_v8",
  filterMtGene = TRUE,
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_gene_expression(), get_clustered_median_junction_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), get_gene_expression(), get_median_exon_expression(), get_median_gene_expression(), get_median_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary()

Examples

## Not run: 
get_top_expressed_genes(tissueSiteDetailId = "Artery_Aorta")

## End(Not run)

Description

Find all transcripts of a reference gene.

• This service returns information about transcripts of the given versioned GENCODE ID.

• A genome build and GENCODE version must be provided.

• By default, this service queries the genome build and GENCODE version used by the latest GTEx release.

GTEx API Portal documentation

Usage

get_transcripts(
  gencodeId,
  gencodeVersion = "v26",
  genomeBuild = "GRCh38/hg38",
  page = 0,
  itemsPerPage = 250
)

Arguments

Value

A tibble.

See Also

Other Reference Genome Endpoints: get_exons(), get_gene_search(), get_genes(), get_genomic_features(), get_gwas_catalog_by_location(), get_neighbor_gene()

Examples

## Not run: 
get_transcripts(gencodeId = "ENSG00000203782.5")

## End(Not run)

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

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)

Description

This service allows the user to query information about variants on a certain chromosome at a certain location.

GTEx Portal API documentation

Usage

get_variant_by_location(
  start,
  end,
  chromosome,
  sortBy = "pos",
  sortDirection = "asc",
  page = 0,
  itemsPerPage = 250
)

Arguments

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()

Examples

get_variant_by_location(start = 153209600,
                        end = 153209700,
                        chromosome = "chr1")