getBenchmarkData imports datasets as TreeSummarizedExperiment objects.
getBenchmarkData(x, dryrun = TRUE)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.
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()
#> 1 HMP_2012_16S_gingival_V13
#> 2 HMP_2012_16S_gingival_V35
#> 3 HMP_2012_16S_gingival_V35_subset
#> 4 HMP_2012_WMS_gingival
#> 5 Stammler_2016_16S_spikein
#> 6 Ravel_2011_16S_BV
#>
#> Use vignette('datasets', package = 'MicrobiomeBenchmarkData') for a detailed description of the datasets.
#>
#> Use getBenchmarkData(dryrun = FALSE) to import all of the datasets.
datasets_names
#> Dataset Dimensions Body.site
#> 1 HMP_2012_16S_gingival_V13 33127 x 311 Gingiva
#> 2 HMP_2012_16S_gingival_V35 17949 x 311 Gingiva
#> 3 HMP_2012_16S_gingival_V35_subset 892 x 76 Gingiva
#> 4 HMP_2012_WMS_gingival 235 x 16 Gingiva
#> 5 Stammler_2016_16S_spikein 247 x 394 Stool
#> 6 Ravel_2011_16S_BV 4036 x 17 Vagina
#> Contrasts
#> 1 Subgingival vs Supragingival plaque.
#> 2 Subgingival vs Supragingival plaque.
#> 3 Subgingival vs Supragingival plaque.
#> 4 Subgingival vs Supragingival plaque.
#> 5 Pre-ASCT (allogeneic stem cell transplantation) vs 14 days after treatment.
#> 6 Healthy vs bacterial vaginosis
#> Biological.ground.truth
#> 1 Enrichment of aerobic taxa in the supragingival plaque and enrichment of anaerobic taxa in the subgingival plaque.
#> 2 Enrichment of aerobic taxa in the supragingival plaque and enrichment of anaerobic taxa in the subgingival plaque.
#> 3 Enrichment of aerobic taxa in the supragingival plaque and enrichment of anaerobic taxa in the subgingival plaque.
#> 4 Enrichment of aerobic taxa in the supragingival plaque and enrichment of anaerobic taxa in the subgingival plaque.
#> 5 Same bacterial loads of the spike-in bacteria across all samples: Salinibacter ruber (extreme halophilic), Rhizobium radiobacter (found in soils and plants), and Alicyclobacillus acidiphilu (thermo-acidophilic).
#> 6 Decrease of Lactobacillus and increase of bacteria isolated during bacterial vaginosis in samples with high Nugent scores (bacterial vaginosis).
## Example 2
dataset <- getBenchmarkData(
"HMP_2012_16S_gingival_V35_subset", dryrun = FALSE
)
#> adding rname 'https://zenodo.org/record/6911027/files/HMP_2012_16S_gingival_V35_subset_count_matrix.tsv'
#> adding rname 'https://zenodo.org/record/6911027/files/HMP_2012_16S_gingival_V35_subset_taxonomy_table.tsv'
#> adding rname 'https://zenodo.org/record/6911027/files/HMP_2012_16S_gingival_V35_subset_taxonomy_tree.newick'
#> Finished HMP_2012_16S_gingival_V35_subset.
dataset[[1]]
#> class: TreeSummarizedExperiment
#> dim: 892 76
#> metadata(0):
#> assays(1): counts
#> rownames(892): OTU_97.31247 OTU_97.44487 ... OTU_97.45365 OTU_97.45307
#> rowData names(7): kingdom phylum ... genus taxon_annotation
#> colnames(76): 700023057 700023179 ... 700114009 700114338
#> colData names(13): dataset subject_id ... sequencing_method
#> variable_region_16s
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowLinks: a LinkDataFrame (892 rows)
#> rowTree: 1 phylo tree(s) (892 leaves)
#> colLinks: NULL
#> colTree: NULL