get_gene_expression {gtexr} | R Documentation |
Get Gene Expression
Description
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.
Usage
get_gene_expression(
gencodeIds,
datasetId = "gtex_v8",
tissueSiteDetailIds = NULL,
attributeSubset = NULL,
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
|
attributeSubset |
String. Examples include but are not limited to "sex", "ageBracket" |
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_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:
# multiple genes, selected tissues
get_gene_expression(gencodeIds = c("ENSG00000132693.12",
"ENSG00000203782.5"),
tissueSiteDetailIds = c("Thyroid", "Whole_Blood"))
# single gene, selected (single) tissue
get_gene_expression(gencodeIds = "ENSG00000132693.12",
tissueSiteDetailIds = "Whole_Blood")
# subset by sex
get_gene_expression(gencodeIds = "ENSG00000132693.12",
tissueSiteDetailIds = "Whole_Blood",
attributeSubset = "sex")
# subset by age bracket
get_gene_expression(gencodeIds = "ENSG00000132693.12",
tissueSiteDetailIds = "Whole_Blood",
attributeSubset = "ageBracket")
## End(Not run)