initDGEobjDef {DGEobj}

Instantiate a class DGEobjDef object.

Description

Instantiate a class DGEobjDef object.

Usage

initDGEobjDef(levels, primaryAssayNames, types, uniqueTypes)

Arguments

levels

A character string or vector providing names for new levels

primaryAssayNames

A character string or vector, must be the same length as levels This argument supplies the primaryAssayNames for the corresponding levels.

types

A named character vector of new types where the values indicate the basetype for each named type (optional)

uniqueTypes

A name or vector of names to add to the uniqueType list (optional)

Value

A class DGEobjDef object suitable for use with initDGEobj

Examples

    # return the default DGEobj definition
    myDGEobjDef <- initDGEobjDef()

    # Optionally add some new types and levels for metabolomics data
     myDGEobjDef <- initDGEobjDef(levels = "metabolomics",
                                  primaryAssayNames = "intensity",
                                  types <- c(normalizedIntensity = "assay"))

    # When a new level is defined, the itemNames and types for the
    # rowData and colData are automatically established.  The
    # types argument is only needed to define downstream workflow objects.