R/MicrobiomeExperiment-class.R

In HCBravoLab/metagenomeSE:

## Class constructor
.MicrobiomeExperiment <- setClass("MicrobiomeExperiment",
    contains="SummarizedExperiment",
    representation(
        rowData="MicrobiomeFeatures"
    )
)

#'
#' The MicrobiomeExperiment representation class
#'
#' SummarizedExperiment-like class for microbiome data. rowData is
#' a MicrobiomeFeatures object LINK so it includes: a taxonomy table
#' (DataFrame), #' optional phylogentic tree (phylo object), and a sequence
#' database.
#'
#' It supports (most) of the interface to phyloseq objects
#'
#' @include MicrobiomeFeatures-class.R
#' @importClassesFrom metagenomeFeatures mgFeatures
#' @importClassesFrom SummarizedExperiment SummarizedExperiment
#'
#' @examples
#'
#' library(metagenomeFeatures)
#' data(mock_mgF)
#'
#' sampleNames <- letters[1:4]
#' pd <- DataFrame(a=letters[1:4], b=1:4)
#' numcounts <- nrow(mock_mgF) * 4
#' counts <- matrix(sample(1:1000,numcounts,replace=TRUE), nr=nrow(mock_mgF), nc=4)
#'
#' MicrobiomeExperiment(assays=SimpleList(counts=counts),
#' rowData=mock_mgF,
#' colData=pd
#' )
#'
#' @aliases MicrobiomeExperiment-class
#' @export
MicrobiomeExperiment <- function(assays = SimpleList(),
    rowData = MicrobiomeFeatures(), ...) {

    if (is.data.frame(rowData) || is(rowData, "DataFrame"))
        rowData <- as(rowData, "MicrobiomeFeatures")

    SummarizedExperiment <-
        if (!is(assays, "SummarizedExperiment"))
            SummarizedExperiment(assays = assays, ...)
        else
            assays

    .MicrobiomeExperiment(SummarizedExperiment, rowData = rowData)
}