get_dataset_raw_expression: Retrieve raw expression data 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 raw expression data of a dataset

Description

Retrieve raw expression data of a dataset

Usage

get_dataset_raw_expression(
  dataset,
  quantitationType,
  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
quantitationType	Quantitation type id. These can be acquired using get_dataset_quantitation_types function. This endpoint can only return non-processed quantitation types.
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 is FALSE (default), a data table of the expression matrix for the queried dataset. If raw is TRUE, returns the binary file in raw form.

Examples

q_types <- get_dataset_quantitation_types("GSE59918")
get_dataset_raw_expression("GSE59918", q_types$id[q_types$name == "Counts"])

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