% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/vaginal_meta-data.R
\docType{data}
\name{vaginal_meta}
\alias{vaginal_meta}
\title{Sample metadata of two public vaginal studies}
\format{A \code{data.frame} of per-sample metadata information}
\source{
\code{\link[curatedMetagenomicData]{curatedMetagenomicData}}
}
\usage{
data(vaginal_meta)
}
\description{
Metadata information of vaginal samples in the two public studies provided in
\code{\link[curatedMetagenomicData]{curatedMetagenomicData}}.
}
\examples{
data(vaginal_meta)
# has vaginal samples across two studies
table(vaginal_meta$studyID, vaginal_meta$body_site)
# The following were used to generate the object
# library(curatedMetagenomicData)
# library(phyloseq)
# datasets <- curatedMetagenomicData(
#   "*metaphlan_bugs_list.vagina*",
#   dryrun = FALSE)
# Construct phyloseq object from the five datasets
# physeq <-
  # Aggregate the five studies into ExpressionSet
#   mergeData(datasets) \%>\%
  # Convert to phyloseq object
#   ExpressionSet2phyloseq() \%>\%
  # Subset features to species
#   subset_taxa(!is.na(Species) & is.na(Strain)) \%>\%
  # Normalize abundances to relative abundance scale
#   transform_sample_counts(function(x) x / sum(x)) \%>\%
  # Filter features to be of at least 1e-5 relative abundance in two samples
#   filter_taxa(kOverA(2, 1e-5), prune = TRUE)
# vaginal_meta <- data.frame(sample_data(physeq))
# vaginal_meta$studyID <- factor(vaginal_meta$studyID)
}
\references{
Pasolli, Edoardo, Lucas Schiffer, Paolo Manghi, Audrey Renson, 
Valerie Obenchain, Duy Tin Truong, Francesco Beghini et al. "Accessible, 
curated metagenomic data through ExperimentHub." Nature methods 14, no. 11 
(2017): 1023.
}
\keyword{datasets}
