get_dataset_quantitation_types: Retrieve quantitation types of a dataset

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

Retrieve quantitation types of a dataset

Description

Retrieve quantitation types of a dataset

Usage

get_dataset_quantitation_types(
  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 containing the quantitation types

The fields of the output data.table are:

• id: If of the quantitation type. Any raw quantitation type can be accessed by get_dataset_raw_expression function using this id.

• name: Name of the quantitation type

• description: Description of the quantitation type

• type: Type of the quantitation type. Either raw or processed. Each dataset will have one processed quantitation type which is the data returned using get_dataset_processed_expression

• ratio: Whether or not the quanitation type is a ratio of multiple quantitation types. Typically TRUE for processed TWOCOLOR quantitation type.

• preferred: The preferred raw quantitation type. This version is used in generation of the processed data within gemma.

• recomputed: If TRUE this quantitation type is generated by recomputing raw data files Gemma had access to.

Examples

get_dataset_quantitation_types("GSE59918")

PavlidisLab/gemma.R documentation built on Oct. 25, 2024, 10:59 a.m.