Get one or more experiments (GSE, SRP, etc) from RefineBio
Source:R/get_refinebio.R
get_refinebio.Rd
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 SummarizedExperiment
s representing the
experiments in the RefineBio downloaded dataset.
Examples
if (FALSE) { # \dontrun{
# 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"
)
} # }