DGEobj-package: DGEobj Package Overview
In DGEobj: Differential Gene Expression (DGE) Analysis Results Data Object

DGEobj-package

R Documentation

DGEobj Package Overview

Description

DGEobj is an S3 data class that provides a flexible container for Differential Gene Expression (DGE) analysis results. The DGEobj class is designed to be extensible allowing definition of new data types as needed. 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.

Details

Operationally, the DGEobj is influenced by the RangedSummarizedExperiment (RSE). The DGEobj has data slots for row (gene), col (samples), assays (anything with n-rows by m-samples dimensions) and metadata (anything that can't be keyed to row, col or assay). The key motivation for creating the DGEobj data structure is that the RSE only allows one data item each in the row and col slots and thus is unsuitable for capturing the plethora of data objects created during a typical DGE workflow. The DGEobj data structure can hold any number of row and col data objects and thus is suitable for capturing the multiple steps of a downstream analysis.

Certain object types, primarily the count matrix and associated row and column info, are defined as unique which means only one instance of that type may be added to the DGEobj.

When multiple objects of one type are included in a DGEobj (e.g. two different fits), the concept of parent attributes is used to associate downstream data objects (e.g. contrasts) with the appropriate data object they are derived from.