Differential Gene Expression (DGE) Analysis Results Data Object
Returns and prints the list of all defined types
Subset with square brackets
Subset internal row or column data
Retrieve data items by baseType
Retrieve a data item by name
Retrieve multiple data items by name
Retrieve data items by type
Initialize with base data (primaryAssayData, row annotations, col anno...
Instantiate a class DGEobjDef object.
Retrieve the object inventory
Add a new type definition to a DGEobj
Print the Inventory
Reset to original data
Removes a named data item
Set attributes
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Retrieve the Key/Value metadata attributes that have a character value...
Add a data item
Add multiple data items
Add annotations
Cast as a simple list
Get the baseType of an internal data item
Get a list of the available baseTypes
DGEobj Package Overview
Get the "assay" dimensions (row/genes by col/samples)
Get the "assay" names (row/genes by col/samples)
Get all attributes
Provides a flexible container to manage and annotate Differential Gene Expression (DGE) analysis results (Smythe et. al (2015) <doi:10.1093/nar/gkv007>). The DGEobj has data slots for row (gene), col (samples), assays (matrix n-rows by m-samples dimensions) and metadata (not keyed to row, col, or assays). A set of accessory functions to deposit, query and retrieve subsets of a data workflow has been provided. Attributes are used to capture metadata such as species and gene model, including reproducibility information such that a 3rd party can access a DGEobj history to see how each data object was created or modified. Since the DGEobj is customizable and extensible it is not limited to RNA-seq analysis types of workflows -- it can accommodate nearly any data analysis workflow that starts from a matrix of assays (rows) by samples (columns).