mia provides various datasets derived from independent experimental studies. The datasets represent instances of the TreeSummarizedExperiment and MultiAssayExperiment containers and can serve as tools to practice the mia functionality.
Currently, the following datasets are available:
dmn_se: A SummarizedExperiment with 130 features and
278 samples
enterotype: A TreeSummarizedExperiment with 553
features and 280 samples
esophagus: A TreeSummarizedExperiment with 58 features
and 3 samples
GlobalPatterns: A TreeSummarizedExperiment with 19216
features and 26 samples
HintikkaXOData: A MultiAssayExperiment with 3
experiments (microbiota, metabolites and biomarkers)
peerj13075: A TreeSummarizedExperiment with 674
features and 58 samples
Tengeler2020: A TreeSummarizedExperiment with 151
features and 27 samples
# Load dataset from mia
library(mia)
data("GlobalPatterns", package = "mia")
# In this case, the dataset is a TreeSE, so it is renamed as tse
tse <- GlobalPatterns
# Print summary
tse
#> class: TreeSummarizedExperiment
#> dim: 19216 26
#> metadata(0):
#> assays(1): counts
#> rownames(19216): 549322 522457 ... 200359 271582
#> rowData names(7): Kingdom Phylum ... Genus Species
#> colnames(26): CL3 CC1 ... Even2 Even3
#> colData names(7): X.SampleID Primer ... SampleType Description
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowLinks: a LinkDataFrame (19216 rows)
#> rowTree: 1 phylo tree(s) (19216 leaves)
#> colLinks: NULL
#> colTree: NULL