getBenchmarkData: Get dataset

In waldronlab/MicrobiomeBenchmarkData: Datasets for benchmarking in microbiome research

Get dataset

Description

getBenchmarkData imports datasets as TreeSummarizedExperiment objects.

Usage

getBenchmarkData(x, dryrun = TRUE)

Arguments

x	A character vector with the name(s) of the dataset(s). If empty and dryrun = TRUE, it returns a message with the names of the available datasets. If empty and dryrun = FALSE, it returns a list of TreeSummarizedExperiments with all of the datasets.
dryrun	If TRUE, only returns a message and invisibly returns the names of the datasets as a character vector. If FALSE, it returns the TreeSummarizedExperiment datasets indicated in the argument 'x'.

Value

A list of TreeSummarizedExperiments when dryrun = FALSE. A data frame with the datasets characteristics when dryrun = TRUE.

Examples

## Example 1
datasets_names <- getBenchmarkData()
datasets_names

## Example 2
dataset <- getBenchmarkData(
    "HMP_2012_16S_gingival_V35_subset", dryrun = FALSE
)
dataset[[1]]

waldronlab/MicrobiomeBenchmarkData documentation built on May 2, 2024, 1:20 p.m.