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#' Microarray design file
#'
#' A microarray design file dataset for cynomolgus macaques infected with M.
#' tuberculosis. Contains sample information such as time point and clinical
#' status.
#'
#' @format A data frame with 30 rows and 7 variables. \describe{
#' \item{columnname}{names matching column names in expression dataset}
#' \item{monkey_id}{id assigned to annotate each monkey}
#' \item{timepoint}{times at which samples were drawn, in days}
#' \item{timerange}{groups time points into stages} \item{sample_id}{id
#' assigned to annotate each sample} \item{clinical_status}{denotes if disease
#' is active or latent} }
#' @source \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84152}
"tb.design"
#' Microarray data on cynomolgus macaques infected with M. tuberculosis
#'
#' A microarray dataset on cynomolgus macaques infected with M. tuberculosis.
#' The study was conducted on 38 monkeys at 11 unequally spaced time points. The
#' dataset presented is a subset of the full dataset.
#'
#' @format A data frame with 4000 rows and 30 columns, where each row is a probe
#' and each column a sample.
#'
#' @source \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84152}
"tb.expr"
#' Flow data on cynomolgus macaques infected with M. tuberculosis
#'
#' A dataset containing flow variables of absolute counts and percentages.
#'
#' @format A data frame with 13 rows of flow variables and 213 columns of
#' samples
#'
#' @source \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84152}
"tb.flow"
#' Flow design file
#'
#' A flow design file dataset for cynomolgus macaques infected with M.
#' tuberculosis. Contains sample information such as time point and clinical
#' status.
#'
#' @format A data frame with 213 rows of samples and 7 variables. \describe{
#' \item{columnname}{names matching column names in expression dataset}
#' \item{monkey_id}{id assigned to annotate each monkey}
#' \item{timepoint}{times at which samples were drawn, in days}
#' \item{timerange}{groups time points into stages} \item{sample_id}{id
#' assigned to annotate each sample} \item{clinical_status}{denotes if disease
#' is active or latent} }
#'
#' @source \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84152}
"tb.flow.des"
#' Baylor Modules
#'
#' A list containing the baylor modules (gene sets)
#'
#' @format A large list containing 260 gene sets.
#'
#' @source baylor modules
"modules"
#' Gene Symbols
#'
#' A vector of gene symbols to match the probes ids in expression
#'
#' @format A vector of 1000 gene symbols
#'
#' @source Illumina
"gene.symbols"
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