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 = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

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). Set globally to maximum value 100000 with options(list(gtexr.itemsPerPage = 100000)).

.verbose

Logical. If TRUE (default), print paging information. Set to FALSE globally with options(list(gtexr.verbose = FALSE)).

.return_raw

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

Value

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

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 0.2.0 Index]