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| #' \code{teamlahti} Package. | ||
| #' | ||
| #' \code{teamlahti} aims to develop [R/Bioconductor](https://www.bioconductor.org/) | ||
| #' tools to analyze AMR data by integrating publicly available human gut | ||
| #' metagenomes with ARG profiles (e.g. | ||
| #' [metagenomics](https://www.nature.com/subjects/metagenomics)) and | ||
| #' epidemiological, transmission data to study AMR gene co-migration. | ||
| #' | ||
| #' @name teamlahti-package | ||
| "_PACKAGE" | ||
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| #' teamlahti datasets | ||
| #' | ||
| #' 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: | ||
| #' \itemize{ | ||
| #' \item{\code{\link{Lee2023}}: A TreeSummarizedExperiment with 9,251 samples} | ||
| #' } | ||
| #' | ||
| #' @name teamlahti-datasets | ||
| #' @docType data | ||
| #' @keywords datasets | ||
| #' | ||
| #' @examples | ||
| #' # 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 | ||
| NULL | ||
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| #' Metagenome assembly data | ||
| #' | ||
| #' Lee2023 includes a total of 9,251 human microbiome samples from multiple body | ||
| #' sites (7718 stool, 783 oral cavity, 410 skin, 150 airway, 93 nasal cavity, | ||
| #' 88 vagina, and 9 milk) which had been sequenced in various studies. | ||
| #' | ||
| #' @format A TreeSummarizedExperiment with 4182 features and 5195 samples. The | ||
| #' rowData contains taxonomic information at Kingdom, Phylum, Class, Order, | ||
| #' Family and Genus level. The colData includes: | ||
| #' | ||
| #' \describe{ | ||
| #' \item{Tier_1.Exclusion_before_analysis} | ||
| #' \item{Tier_2.Recover_all_40_SCGs} | ||
| #' \item{Tier_3.Adult_stool_from_well_sampled_countries} | ||
| #' \item{Tier_4.Adult_stool_from_healthy_subjects_not_currently_on_antibiotic} | ||
| #' \item{Study} | ||
| #' \item{Sample_ID} | ||
| #' \item{Sample_assembly_ID} | ||
| #' \item{NumReads} | ||
| #' \item{NumBases} | ||
| #' \item{MedianReadLength} | ||
| #' \item{BodySite} | ||
| #' \item{BodySubsite} | ||
| #' \item{AgeYears} | ||
| #' \item{AgeCategory} | ||
| #' \item{InfantAge} | ||
| #' \item{Westernized} | ||
| #' \item{Country} | ||
| #' \item{Gender} | ||
| #' \item{BMI} | ||
| #' \item{Disease} | ||
| #' \item{antibiotic_exposure_status_descriptive} | ||
| #' \item{antibiotic_current_use_binary} | ||
| #' } | ||
| #' | ||
| #' @name Lee2023 | ||
| #' @docType data | ||
| #' @keywords datasets | ||
| #' @usage data(Lee2023) | ||
| #' @seealso \code{\link{teamlahti-datasets}} | ||
| #' @author Lee, K., Raguideau, S., Sirén, K. et al. | ||
| #' @references | ||
| #' Lee, K., Raguideau, S., Sirén, K. et al. | ||
| #' Population-level impacts of antibiotic usage on the human gut microbiome. | ||
| #' Nat Commun 14, 1191 (2023). \url{https://doi.org/10.1038/s41467-023-36633-7} | ||
| #' | ||
| NULL |
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