R/Hadza.R

In SQMtools: Analyze Results Generated by the 'SqueezeMeta' Pipeline

#' Hadza hunter-gatherer gut metagenomes
#'
#' Subset of two bins (and the associated contigs and genes)
#' generated by running SqueezeMeta on two gut metagenomic samples
#' obtained from two hunter-gatherers of the Hadza ethnic group.
#'
#' @docType data
#'
#' @usage data(Hadza)
#'
#' @format A SQM object; see \code{\link{loadSQM}}.
#'
#' @keywords datasets
#'
#' @references Rampelli \emph{et al.}, 2015. Metagenome Sequencing of the Hadza
#' Hunter-Gatherer Gut Microbiota. \emph{Curr. biol.} \bold{25}:1682-93
#' (\href{https://pubmed.ncbi.nlm.nih.gov/25981789/}{PubMed}).
#'
#' @source \href{https://www.ncbi.nlm.nih.gov/sra/?term=SRR1927149}{SRR1927149}, \href{https://www.ncbi.nlm.nih.gov/sra/?term=SRR1929485}{SRR1929485}.
#'
#' @examples
#' data(Hadza)
#' plotTaxonomy(Hadza, "genus", rescale=TRUE)
#' plotFunctions(Hadza, "COG")
#'
"Hadza"