get_gene_probes: Retrieve the probes associated to a genes across all...

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

Retrieve the probes associated to a genes across all platforms

Description

Retrieve the probes associated to a genes across all platforms

Usage

get_gene_probes(
  gene,
  offset = 0L,
  limit = 20L,
  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
offset	The offset of the first retrieved result.
limit	Defaults to 20. Limits the result to specified amount of objects. Has a maximum value of 100. Use together with offset and the totalElements attribute in the output to compile all data if needed.
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 probes representing a gene across all platrofms. A list if raw = TRUE. A 404 error if the given identifier does not map to any genes.

The fields of the output data.table are:

• element.name: Name of the element. Typically the probeset name

• element.description: A free text field providing optional information about the element

• platform.shortName: Shortname of the platform given by Gemma. Typically the GPL identifier.

• platform.name: Full name of the platform

• platform.ID: Id number of the platform given by Gemma

• platform.type: Type of the platform.

• platform.description: Free text field describing the platform.

• platform.troubled: Whether the platform is marked as troubled by a Gemma curator.

• taxon.name: Name of the species platform was made for

• 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 underyling database used in Gemma for the taxon

Examples

get_gene_probes(1859)

PavlidisLab/Gemma-API documentation built on Oct. 25, 2024, 10:25 a.m.