gtexr (version 0.2.1)

get_top_expressed_genes: Get Top Expressed Genes

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

Value

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

Arguments

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.

datasetId

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

filterMtGene

Logical. Exclude mitochondrial genes.

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

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

if (FALSE) { # identical(Sys.getenv("IN_PKGDOWN"), "true")
get_top_expressed_genes(tissueSiteDetailId = "Artery_Aorta")
}