get_dataset_expression_for_genes: Retrieve the expression data matrix of a set of datasets and...

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

Retrieve the expression data matrix of a set of datasets and genes

Description

Retrieve the expression data matrix of a set of datasets and genes

Usage

get_dataset_expression_for_genes(
  datasets,
  genes,
  keepNonSpecific = FALSE,
  consolidate = NA_character_,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

datasets	A vector of dataset IDs or short names
genes	A vector of NCBI IDs, Ensembl IDs or gene symbols.
keepNonSpecific	logical. FALSE by default. If TRUE, results from probesets that are not specific to the gene will also be returned.
consolidate	An option for gene expression level consolidation. If empty, will return every probe for the genes. "pickmax" to pick the probe with the highest expression, "pickvar" to pick the prove with the highest variance and "average" for returning the average expression
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 list of data frames

Examples

get_dataset_expression_for_genes("GSE2018", genes = c(10225, 2841))

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