search_gemma: Search everything in Gemma

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

Search everything in Gemma

Description

Search everything in Gemma

Usage

search_gemma(
  query,
  taxon = NA_character_,
  platform = NA_character_,
  limit = 100,
  resultType = "experiment",
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

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
platform	A platform numerical identifier or a platform short name
limit	Defaults to 100 with a maximum value of 2000. Limits the number of returned results. Note that this function does not support pagination.
resultType	The kind of results that should be included in the output. Can be experiment, gene, platform or a long object type name, documented in the API documentation.
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

If raw = FALSE and resultType is experiment, gene or platform, a data.table containing the search results. If it is any other type, a list of results. A list with additional details about the search if raw = TRUE

Examples

search_gemma("bipolar")

PavlidisLab/gemma.R documentation built on May 1, 2024, 10:48 p.m.