get_genes: Retrieve genes matching gene identifiers

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

Retrieve genes matching gene identifiers

Description

Retrieve genes matching gene identifiers

Usage

get_genes(
  genes,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

genes	A vector of NCBI IDs, Ensembl IDs or gene symbols.
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

A data table with information about the querried gene(s) A list if raw = TRUE.

The fields of the output data.table are:

• gene.symbol: Symbol for the gene

• gene.ensembl: Ensembl ID for the gene

• gene.NCBI: NCBI id for the gene

• gene.name: Name of the gene

• gene.aliases: Gene aliases. Each row includes a vector

• gene.MFX.rank: Multifunctionality rank for the gene

• taxon.name: Name of the species

• taxon.scientific: Scientific name for the taxon

• taxon.ID: Internal identifier given to the species by Gemma

• taxon.NCBI: NCBI ID of the taxon

• taxon.database.name: Underlying database used in Gemma for the taxon

• taxon.database.ID: ID of the underlying database used in Gemma for the taxon

Examples

get_genes("DYRK1A")
get_genes(c("DYRK1A", "PTEN"))

PavlidisLab/Gemma-API documentation built on Dec. 15, 2024, 12:45 a.m.