get_clustered_median_exon_expression {gtexr}R Documentation

Get Clustered Median Exon Expression

Description

Find median transcript expression data along with hierarchical clusters.

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
)

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.

Value

A tibble, with clustering data stored as an attribute, "clusters".

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

## Not run: 
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)

## End(Not run)

[Package gtexr version 0.1.0 Index]