newDeaSet {RegEnrich} | R Documentation

## DeaSet object creator

### Description

DeaSet object creator

### Usage

    newDeaSet(
      assayRaw = matrix(nrow = 0, ncol = 0),
      rowData = NULL,
      assays = SimpleList(),
      colData = DataFrame(),
      metadata = list()
    )

### Arguments

`assayRaw` | A matrix of gene expression data. This can be the same as the matrix-like element in `assays` parameter.
`rowData` | A DataFrame object describing the rows.
`assays` | A list or SimpleList of matrix-like element, or a matrix-like object. The matrix-like element can be the same as `assayRaw` parameter.
`colData` | A DataFrame describing the sample information.
`metadata` | An optional list of arbitrary content describing the overall experiment.

### Value

A DeaSet object.

### Examples

    # Empty DeaSet object
    newDeaSet()

    # 100 * 6 DeaSet object
    nrows = 100
    ncols = 6
    counts = matrix(rnbinom(nrows * ncols, size = 2, mu = 500),
                    nrow = nrows)
    assays = SimpleList(counts=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))
    newDeaSet(assayRaw = counts,
              rowData = elementMetadata,
              assays = SimpleList(assayData = counts),
              colData = colData)

[Package RegEnrich version 1.2.0 Index]