teamlahti provides Lee2023 dataset derived from independent experimental studies.The dataset represents instances of the TreeSummarizedExperiment to serve as tools to practice the teamlahti functionality.
Currently, the following datasets are available:
Lee2023: A TreeSummarizedExperiment with 9,251 samples
# Load dataset from teamlahti
library(teamlahti)
data("Lee2023", package = "teamlahti")
# In this case, the dataset is a TreeSE, so it is renamed as tse
tse <- Lee2023
# Print summary
tse
#> class: TreeSummarizedExperiment
#> dim: 4182 5195
#> metadata(1): Country
#> assays(1): relabundance
#> rownames(4182): 362 363 ... 23727 23733
#> rowData names(13): sgbid sgbname ... assigned_pathogen_name
#> assigned_pathogen_taxid
#> colnames(5195): AsnicarF_2017__MV_FEM1_t1Q14
#> AsnicarF_2017__MV_FEM2_t1Q14 ... ZellerG_2014__CCMD74930188ST-21-0
#> ZellerG_2014__CCMD79987997ST-21-0
#> colData names(22): Tier_1.Exclusion_before_analysis
#> Tier_2.Recover_all_40_SCGs ... antibiotic_exposure_status_descriptive
#> antibiotic_current_use_binary
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(2): read assembly
#> rowLinks: NULL
#> rowTree: NULL
#> colLinks: NULL
#> colTree: NULL