dot-get_gene_differential_expression_values_in_taxon: Retrieve the differential expression results for a given gene...

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

Retrieve the differential expression results for a given gene and taxa among datasets matching the provided query and filter

Description

Retrieve the differential expression results for a given gene and taxa among datasets matching the provided query and filter

Usage

.get_gene_differential_expression_values_in_taxon(
  gene,
  query = NA_character_,
  taxon = NA_character_,
  uris = NA_character_,
  filter = NA_character_,
  threshold = 1,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

gene	An ensembl gene identifier which typically starts with ensg or an ncbi gene identifier or an official gene symbol approved by hgnc
query	The search query. Queries can include plain text or ontology terms They also support conjunctions ("alpha AND beta"), disjunctions ("alpha OR beta") grouping ("(alpha OR beta) AND gamma"), prefixing ("alpha*"), wildcard characters ("BRCA?") and fuzzy matches ("alpha~").
taxon	A numerical taxon identifier or an ncbi taxon identifier or a taxon identifier that matches either its scientific or common name
uris	A vector of ontology term URIs. Providing multiple terms will return results containing any of the terms and their children. These are appended to the filter and equivalent to filtering for allCharacteristics.valueUri
filter	Filter results by matching expression. Use filter_properties function to get a list of all available parameters. These properties can be combined using "and" "or" clauses and may contain common operators such as "=", "<" or "in". (e.g. "taxon.commonName = human", "taxon.commonName in (human,mouse), "id < 1000")
threshold	number
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

PavlidisLab/Gemma-API documentation built on April 14, 2025, 11:31 a.m.