DeaSet-class: DeaSet class
In WTaoUMC/RegEnrich: Gene regulator enrichment analysis

DeaSet class

colData: DataFrame object, sample information, the row name is corresponding to the column names of expression matrix in the assays slot.
assays: SimpleList object of one/multiple matrix/matrices, this is the slot for storing the expression data after filtering (and after Variance Stabilizing Transformation, i.e. VST, if the differential analysis method is 'Wald_DESeq2' or 'LRT_DESeq2'). And the expression matrix is used for network inference and plotting.
NAMES: row names of expression data in assays slot and elementMetadata slot.
elementMetadata: feature information, contains at least a DataFrame of three columns, i.e. 'gene', 'p' and 'logFC', which stores gene names/IDs, differential p values and log2 expression fold changes, respectively.
metadata: DataFrame object, information of feature columns.
assayRaw: a slot for saving the raw expression data.

nrows = 100
ncols = 6
counts = matrix(rnbinom(nrows * ncols, size = 2, mu = 500),
                nrow = nrows)
assays = SimpleList(assayData = counts)

colData = DataFrame(Condition = rep(c("treatment", "ctrl"), 3),
                    row.names=LETTERS[1:6])
geneNames = sprintf("G%03s", seq(nrows))
elementMetadata = DataFrame(gene = geneNames,
                            p = numeric(nrows),
                            logFC = numeric(nrows))

ds = new("DeaSet",
         assays = Assays(assays),
         colData = colData,
         assayRaw = counts,
         elementMetadata = elementMetadata,
         NAMES = geneNames)
ds