DeaSet-class {RegEnrich} | R Documentation

## DeaSet class

### Description

DeaSet class

### Slots

`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.

### Examples

    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

[Package RegEnrich version 1.4.0 Index]