DeaSet-class {RegEnrich} | R Documentation |
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