get_clustered_median_junction_expression {gtexr}R Documentation

Get Clustered Median Junction Expression

Description

Find median junction expression data along with hierarchical clusters.

By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_clustered_median_junction_expression(
  gencodeIds,
  datasetId = "gtex_v8",
  tissueSiteDetailIds = NULL,
  .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.

.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_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_junction_expression(gencodeIds = c(
  "ENSG00000203782.5",
  "ENSG00000132693.12"
))

# clustering data is stored as an attribute "clusters"
result <- get_clustered_median_junction_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 0.2.0 Index]