get_single_nucleus_gex: Get Single Nucleux Gex

In gtexr: Query the GTEx Portal API

Get Single Nucleux Gex

Description

Retrieve Single Nucleus Gene Expression Data for a given Gene.

GTEx Portal API documentation

Usage

get_single_nucleus_gex(
  gencodeIds,
  datasetId = "gtex_snrnaseq_pilot",
  tissueSiteDetailIds = NULL,
  excludeDataArray = TRUE,
  page = 0,
  itemsPerPage = 250
)

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.
excludeDataArray	String. Options are TRUE or FALSE
page	Integer (default = 0).
itemsPerPage	Integer (default = 250).

Value

A tibble

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_summary(), get_top_expressed_genes()

Examples

## Not run: 
# Search for one or more genes - returns a tibble with one row per tissue.
# Column "cellTypes" now contains a tibble of expression summary data, with
# one row for each cell type
get_single_nucleus_gex(gencodeIds = c("ENSG00000203782.5",
                                      "ENSG00000132693.12"))

# `excludeDataArray = FALSE` - expression values are stored under "celltypes"
# in an additional column called "data"
response <- get_single_nucleus_gex(gencodeIds = "ENSG00000132693.12",
                                   excludeDataArray = FALSE,
                                   itemsPerPage = 2)

response

# "cellTypes" contains a tibble of data with one row for each
# cell type e.g. for Breast_Mammary_Tissue
response$cellTypes[[2]]

# when `excludeDataArray = FALSE`, expression values are stored in "data"
# e.g. for Breast_Mammary_Tissue, Epithelial cell (luminal):
response$cellTypes[[2]]$data[[1]]

## End(Not run)

gtexr documentation built on Sept. 19, 2024, 5:06 p.m.