get_refinebio: Get one or more experiments (GSE, SRP, etc) from RefineBio

In seandavi/RefineBio: The bridge between refine.bio and Bioconductor

Get one or more experiments (GSE, SRP, etc) from RefineBio

Description

This is the main function for interacting with RefineBio. It will download, extract, and load the data from RefineBio for the given experiment(s).

Usage

get_refinebio(
  experiments,
  quantile_normalize = FALSE,
  svd_algorithm = "NONE",
  scale_by = "NONE",
  aggregate_by = "EXPERIMENT"
)

Arguments

quantile_normalize	logical Should the data be quantile normalized? Default is FALSE. If TRUE, the data will be quantile normalized based on the distribution of all data for a species.
svd_algorithm	character Which SVD algorithm to use? One of "NONE", "RANDOMIZED", "ARPACK"
scale_by	character How to scale the data? One of "NONE", "MINMAX", "STANDARD", "ROBUST"
aggregate_by	character How to aggregate the data? One of "EXPERIMENT", "SPECIES", "ALL"
experiment	character() vector of experiment IDs (e.g., GSE1133)s

Value

A list of SummarizedExperiments representing the experiments in the RefineBio downloaded dataset.

Author(s)

Sean Davis <seandavi.gmail.com>

Examples

## Not run: 
# Get a single experiment
expt <- get_refinebio("GSE116672")

# Get multiple experiments
expts <- get_refinebio(c("SRP066613", "SRP158666"))

# Get multiple experiments with quantile normalization
expts <- get_refinebio(
  c("SRP066613", "SRP158666"),
  quantile_normalize = TRUE
)
# Get multiple experiments with quantile normalization and
# aggregate everything into one summarized experiment
expts <- get_refinebio(
  c("SRP066613", "SRP158666"),
  quantile_normalize = TRUE,
  aggregate_by = "ALL"
)

## End(Not run)

seandavi/RefineBio documentation built on June 1, 2025, 4:10 p.m.