get_dataset_platforms: Retrieve the platforms of a dataset

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

Retrieve the platforms of a dataset

Description

Retrieve the platforms of a dataset

Usage

get_dataset_platforms(
  dataset,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

dataset	A numerical dataset identifier or a dataset short 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

A data table with information about the platform(s). A list if raw = TRUE. A 404 error if the given identifier does not map to any object

The fields of the output data.table are:

• platform.ID: Internal identifier of the platform

• platform.shortName: Shortname of the platform.

• platform.name: Full name of the platform.

• platform.description: Free text description of the platform

• platform.troubled: Whether or not the platform was marked "troubled" by a Gemma process or a curator

• platform.experimentCount: Number of experiments using the platform within Gemma

• platform.type: Technology type for the platform.

• 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_dataset_platforms("GSE2018")

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