,
Levi Waldron [aut] ,
Marcel Ramos [ctb]| Title: | Datasets for benchmarking in microbiome research |
|---|---|
| Description: | The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available. |
| Authors: | Samuel Gamboa [aut, cre] ,
Levi Waldron [aut] ,
Marcel Ramos [ctb] |
| Maintainer: | Samuel Gamboa <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.7.1 |
| Built: | 2024-09-03 01:01:36 UTC |
| Source: | https://github.com/waldronlab/MicrobiomeBenchmarkData |
getBenchmarkData imports datasets as TreeSummarizedExperiment objects.
getBenchmarkData(x, dryrun = TRUE)getBenchmarkData(x, dryrun = TRUE)
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'. |
A list of TreeSummarizedExperiments when dryrun = FALSE. A data frame with the datasets characteristics when dryrun = TRUE.
## Example 1 datasets_names <- getBenchmarkData() datasets_names ## Example 2 dataset <- getBenchmarkData( "HMP_2012_16S_gingival_V35_subset", dryrun = FALSE ) dataset[[1]]## Example 1 datasets_names <- getBenchmarkData() datasets_names ## Example 2 dataset <- getBenchmarkData( "HMP_2012_16S_gingival_V35_subset", dryrun = FALSE ) dataset[[1]]
The MicrobiomeBenchmarkData provide functions for accessing
various microbiome datasets with biological ground truth.
Maintainer: Samuel Gamboa [email protected] (ORCID)
Authors:
Levi Waldron (ORCID)
Other contributors:
Marcel Ramos [contributor]
Useful links:
Report bugs at https://github.com/waldronlab/MicrobiomeBenchmarkData/issues
removeCache removes all files saved in the cache.
removeCache(ask = interactive())removeCache(ask = interactive())
ask |
If TRUE, a prompt will appear asking the user to confirm removal
of cache. Default value is given by the |
NULL The cache and all of its contents are removed.
## Remove cache removeCache()## Remove cache removeCache()
A data frame with the combined metadata of all of the samples in the datasets provided through the MicrobiomeBenchmarkData package.
data("sampleMetadata", package = "MicrobiomeBenchMarkData")data("sampleMetadata", package = "MicrobiomeBenchMarkData")
A data.frame.
The scml function applies the
spike-in-based calibration to total microbial load (SCML) method to
scml(tse, bac = c("s", "r", "a"))scml(tse, bac = c("s", "r", "a"))
tse |
A treeSummarizedExperiment from the |
bac |
A character. One of the following options: s = Salinibacter ruber (AF323500), r = Rhizobium radiobacter (AB247615), a, = Alicyclobacillus acidiphilus (AB076660) |
A TreeSummarizedExperiment with SCML data instead of counts.
tse <- getBenchmarkData("Stammler_2016_16S_spikein", dryrun = FALSE)[[1]] tseSCML <- scml(tse, bac = "s")tse <- getBenchmarkData("Stammler_2016_16S_spikein", dryrun = FALSE)[[1]] tseSCML <- scml(tse, bac = "s")