gtexr (version 0.2.1)

get_clustered_median_exon_expression: Get Clustered Median Exon Expression

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,
  .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.

.return_raw

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

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

if (FALSE) { # identical(Sys.getenv("IN_PKGDOWN"), "true")
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)
}