gtexr (version 0.2.1)

get_median_transcript_expression: Get Median Transcript Expression

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

Value

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

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.

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_single_nucleus_gex(), get_single_nucleus_gex_summary(), get_top_expressed_genes()

Examples

if (FALSE) { # identical(Sys.getenv("IN_PKGDOWN"), "true")
get_median_transcript_expression(gencodeIds = "ENSG00000132693.12")
}