get_gene_expression {gtexr}R Documentation

Get Gene Expression

Description

Find normalized gene expression data.

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

gencodeIds

A character vector of Versioned GENCODE IDs, e.g. c("ENSG00000132693.12", "ENSG00000203782.5").

datasetId

String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot".

tissueSiteDetailIds

Character vector of IDs for tissues of interest. Can be GTEx specific IDs (e.g. "Whole_Blood"; use get_tissue_site_detail() to see valid values) or Ontology IDs.

attributeSubset

String. Examples include but are not limited to "sex", "ageBracket"

page

Integer (default = 0).

itemsPerPage

Integer (default = 250).

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)

[Package gtexr version 0.1.0 Index]