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).
| Version: | 1.0.1 |
| Depends: | R (≥ 3.5.0) |
| Imports: | assertthat, magrittr, stringr, utils, GenomicRanges |
| Suggests: | knitr, rmarkdown, testthat, edgeR |
| Published: | 2020-12-07 |
| Author: | John Thompson [aut], Connie Brett [aut, cre], Isaac Neuhaus [aut], Ryan Thompson [aut] |
| Maintainer: | Connie Brett <connie at aggregate-genius.com> |
| License: | GPL-3 |
| NeedsCompilation: | no |
| Language: | en-US |
| Materials: | README NEWS |
| CRAN checks: | DGEobj results |
| Reference manual: | DGEobj.pdf |
| Vignettes: |
DGEobj Overview |
| Package source: | DGEobj_1.0.1.tar.gz |
| Windows binaries: | r-devel: DGEobj_1.0.1.zip, r-release: DGEobj_1.0.1.zip, r-oldrel: DGEobj_1.0.1.zip |
| macOS binaries: | r-release: DGEobj_1.0.1.tgz, r-oldrel: not available |
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