Differential Gene Expression (DGE) Analysis Results Data Object

Provides a flexible container to manage and annotate Differential Gene Expression (DGE) analysis results (Smythe et. al (2015) ). 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).


Reference manual

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1.0.3 by Connie Brett, 6 months ago

Browse source code at https://github.com/cran/DGEobj

Authors: John Thompson [aut] , Connie Brett [aut, cre] , Isaac Neuhaus [aut] , Ryan Thompson [aut]

Documentation:   PDF Manual  

GPL-3 license

Imports assertthat, magrittr, stringr, utils, GenomicRanges

Suggests conflicted, dplyr, glue, knitr, rmarkdown, testthat, biomaRt, edgeR

Imported by DGEobj.utils.

See at CRAN