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Get Gene Expression

Source: R/get_gene_expression.R
get_gene_expression.Rd

Find normalized gene expression data.

  • Returns normalized gene expression in tissues at the sample level.

  • Results may be filtered by dataset, gene or tissue, but at least one gene must be provided.

By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_gene_expression(
  gencodeIds,
  datasetId = "gtex_v8",
  tissueSiteDetailIds = NULL,
  attributeSubset = NULL,
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .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.

attributeSubset

String. Examples include but are not limited to "sex", "ageBracket"

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

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_junction_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), 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

# multiple genes, selected tissues
get_gene_expression(
  gencodeIds = c(
    "ENSG00000132693.12",
    "ENSG00000203782.5"
  ),
  tissueSiteDetailIds = c("Thyroid", "Whole_Blood")
)
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 4
#> # A tibble: 4 × 8
#>   data        tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit 
#>   <list>      <chr>              <chr>      <chr>     <chr>     <chr>      <chr>
#> 1 <dbl [653]> Thyroid            UBERON:00… gtex_v8   ENSG0000… LOR        TPM  
#> 2 <dbl [755]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… LOR        TPM  
#> 3 <dbl [653]> Thyroid            UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#> 4 <dbl [755]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#> # ℹ 1 more variable: subsetGroup <lgl>

# single gene, selected (single) tissue
get_gene_expression(
  gencodeIds = "ENSG00000132693.12",
  tissueSiteDetailIds = "Whole_Blood"
)
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 1
#> # A tibble: 1 × 8
#>   data        tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit 
#>   <list>      <chr>              <chr>      <chr>     <chr>     <chr>      <chr>
#> 1 <dbl [755]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#> # ℹ 1 more variable: subsetGroup <lgl>

# subset by sex
get_gene_expression(
  gencodeIds = "ENSG00000132693.12",
  tissueSiteDetailIds = "Whole_Blood",
  attributeSubset = "sex"
)
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 1
#> # A tibble: 1 × 8
#>   data        tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit 
#>   <list>      <chr>              <chr>      <chr>     <chr>     <chr>      <chr>
#> 1 <dbl [755]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#> # ℹ 1 more variable: subsetGroup <lgl>

# subset by age bracket
get_gene_expression(
  gencodeIds = "ENSG00000132693.12",
  tissueSiteDetailIds = "Whole_Blood",
  attributeSubset = "ageBracket"
)
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 1
#> # A tibble: 1 × 8
#>   data        tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit 
#>   <list>      <chr>              <chr>      <chr>     <chr>     <chr>      <chr>
#> 1 <dbl [755]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#> # ℹ 1 more variable: subsetGroup <lgl>