dot-get_dataset_expression_for_genes_in_taxon: Retrieve the expression data matrix of a set of datasets and...

In jsicherman/Gemma-API: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Retrieve the expression data matrix of a set of datasets and genes

Description

Retrieve the expression data matrix of a set of datasets and genes

Usage

.get_dataset_expression_for_genes_in_taxon(
  datasets,
  genes,
  keepNonSpecific = FALSE,
  consolidate = NA_character_,
  taxon,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

datasets	A comma-delimited list of dataset IDs or short names. The value may be compressed with gzip and encoded with base64.
genes	A comma-delimited list of NCBI IDs, Ensembl IDs or gene symbols. The value may be compressed with gzip and encoded with base64.
keepNonSpecific	boolean
consolidate	An option for gene expression level consolidation.
taxon	A numerical taxon identifier or an ncbi taxon identifier or a taxon identifier that matches either its scientific or common name
raw	TRUE to receive results as-is from Gemma, or FALSE to enable parsing. Raw results usually contain additional fields and flags that are omitted in the parsed results.
memoised	Whether or not to save to cache for future calls with the same inputs and use the result saved in cache if a result is already saved. Doing options(gemma.memoised = TRUE) will ensure that the cache is always used. Use forget_gemma_memoised to clear the cache.
file	The name of a file to save the results to, or NULL to not write results to a file. If raw == TRUE, the output will be the raw endpoint from the API, likely a JSON or a gzip file. Otherwise, it will be a RDS file.
overwrite	Whether or not to overwrite if a file exists at the specified filename.

Value

Varies

jsicherman/Gemma-API documentation built on April 17, 2025, 4:17 p.m.