Get Single Nucleus Gex Summary

Retrieve Summarized Single Nucleus Gene Expression Data.

GTEx Portal API documentation

Usage

get_single_nucleus_gex_summary(
  datasetId = "gtex_snrnaseq_pilot",
  tissueSiteDetailIds = NULL,
  page = 0,
  itemsPerPage = 250
)

Arguments

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.

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(), get_top_expressed_genes()

Examples

# \dontrun{
# all tissues
get_single_nucleus_gex_summary()
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 114
#> # A tibble: 114 × 5
#>    tissueSiteDetailId ontologyId     datasetId           cellType       numCells
#>    <chr>              <chr>          <chr>               <chr>             <int>
#>  1 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Myocyte (sk. …      769
#>  2 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Myocyte (NMJ-…       95
#>  3 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Endothelial c…     1124
#>  4 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Myocyte (sk. …    20772
#>  5 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Fibroblast         5944
#>  6 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Pericyte/SMC        448
#>  7 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Immune (DC/ma…      721
#>  8 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Adipocyte           159
#>  9 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Schwann cell         35
#> 10 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Satellite cell      487
#> # ℹ 104 more rows

# filter for specific tissue
get_single_nucleus_gex_summary(tissueSiteDetailIds = c("Breast_Mammary_Tissue",
                                                       "Skin_Sun_Exposed_Lower_leg"))
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 25
#> # A tibble: 25 × 5
#>    tissueSiteDetailId         ontologyId     datasetId         cellType numCells
#>    <chr>                      <chr>          <chr>             <chr>       <int>
#>  1 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Epithel…     4849
#>  2 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Adipocy…     1761
#>  3 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Immune …      358
#>  4 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Myoepit…      950
#>  5 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Fibrobl…      819
#>  6 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Endothe…      762
#>  7 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Endothe…      119
#>  8 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Pericyt…      152
#>  9 Skin_Sun_Exposed_Lower_leg UBERON:0004264 gtex_snrnaseq_pi… Sweat g…      300
#> 10 Skin_Sun_Exposed_Lower_leg UBERON:0004264 gtex_snrnaseq_pi… Epithel…       72
#> # ℹ 15 more rows
# }