R/POSTmData.R

In POSTm: Phylogeny-Guided OTU-Specific Association Test for Microbiome Data

#' Example Dataset For Illustration
#'
#' This data set is provided for the purposes of illustrating the use of
#' the software. It was adapted from the vaginal microbiome dataset from 
#' Subramaniam et al. (2016). The original dataset consists of 39 
#' individuals with 19 bacterial vaginosis (BV) patients and 20 healthy controls.
#' The sequencing data and metadata are publicly available at NCBI SRA database
#' (PRJNA600021). Initial data processing, lead to 2711 OTUs formed at 97\%
#' sequence similarity. FastTree (Price et al, 2010) was used to construct the 
#' phylogenetic tree. The OTUs data have been filitered to exclude those with 
#' abundance < 0.005\% and prevalence < 10\%.
#' 
#' 
#' @usage data(POSTmData)
#'
#' @format POSTmData contains 4 objects.
#'  \describe{
#'   \item{metadata}{a data.frame containing 30 participants. The
#'   data.frame contains 3 columns} 
#'   \describe{
#'   \item{SampleID}{Character. Unique participant identifiers.}
#'   \item{mRace}{A dichotomous covariate describing the maternity race.}
#'   \item{GC}{Gestational complication indicator. "BV" indicates that
#'             individual was diagnosed with bacterial vaginosis; "Normal"
#'             otherwise}
#'   }
#'   \item{otu}{a 39 x 189 matrix containing OTU count data}
#'   \item{otutree}{a phylogenetic tree constructed using all 2711 OTU sequences}
#'   \item{otuseq}{a character vector of OTU sequencing data used to construct 
#'                 the phylogenetic tree}
#'   }
#'
#' @name POSTmData
#' @aliases metadata otu otutree otuseq
#' @keywords datasets
NULL