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data.R
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data.R
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#' Gingival data set from the Human Microbiome Project
#' @usage data(hmp_gingival)
#' @format A list with two elements
#' \describe{
#' \item{data}{The microbiome relative abundance data with relevant metadata
#' obtained from the Human Microbiome Project via the \code{HMP16SData}
#' package (snapshot: 11-15-2021).
#' The data set is hosted the container of type
#' \code{phyloseq}. Using the
#' \code{mia} package users can convert it
#' to the \code{TreeSummarizedExperiment} type.}
#' \item{set}{Sets of microbes based on their metabolism
#' annotation at the Genera level.
#' Annotations obtained via Calagaro et al.'s repository on Zenodo
#' (\url{https://doi.org/10.5281/zenodo.3942108})}
#' }
#' @references Data can be downloaded directly from
#' \url{https://hmpdacc.org/hmp/}
#' @references R interface of the data from
#' \url{https://doi.org/doi:10.18129/B9.bioc.HMP16SData}
#' @references Beghini F, Renson A, Zolnik CP, Geistlinger L,
#' Usyk M, Moody TU, et al.
#' Tobacco Exposure Associated with Oral Microbiota
#' Oxygen Utilization in the
#' New York City Health and Nutrition Examination Study.
#' Annals of Epidemiology.
#' 2019;34:18–25.e3. doi:10.1016/j.annepidem.2019.03.005
#' @references Consortium THMP,
#' Huttenhower C, Gevers D,
#' Knight R, Abubucker S, Badger
#' JH, et al. Structure,
#' Function and Diversity of the Healthy Human Microbiome.
#' Nature. 2012;486(7402):207–214. doi:10.1038/nature11234.
#' @references Calgaro M, Romualdi C, Waldron L, Risso D,
#' Vitulo N. Assessment of Statistical
#' Methods from Single Cell, Bulk RNA-Seq, and Metagenomics Applied to
#' Microbiome Data. Genome Biology. 2020;21(1):191.
#' doi:10.1186/s13059-020-02104-1
#' @references Schiffer L, Azhar R,
#' Shepherd L, Ramos M,
#' Geistlinger L, Huttenhower C, et al.
#' HMP16SData: Efficient Access to
#' the Human Microbiome Project through Bioconductor.
#' American Journal of Epidemiology. 2019;doi:10.1093/aje/kwz006.
"hmp_gingival"