Copyright (c)  [Finn Drabløs, Rezvan Ehsani, Casper van Mourik] under the MIT license.
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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GAPGOM (novel Gene Annotation Prediction and other GO Metrics) is an R package with tools and algorithms for estimating correlation of gene expression enriched terms in gene sets, and semantic distance between sets of gene ontology (GO) terms. This package has been made for predicting the annotation of un-annotated gene(s), in particular with respect to GO, and testing such predictions. The prediction is done by comparing expression patterns between a query gene and a library of annotated genes, and annotate the query gene by enriched terms from the set of genes with similar expression pattern (often described as "guilt by association").
For more info, read the package vignette after building and installing the package (This will later be available on Bioconductor).
BiocManager::install("GAPGOM") with Bioconductor version 3.9 or above.
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All notable changes to this project will be documented in this file.
*Changes of commit versions will not be kept track of, instead only major and minor versions will keep a changelog;
x.y.z (e.g. 1.2.5) --> changes of 1.2.z and 1.3.z will be kept track of but not the small "z" version changes, because this changes with every commit. All z changes will be kept track of in the unreleased minor (y) version. There was an exception for the first version however, because this version didn't use correct convention yet (0.0.1). Failed implementations might be re-evaluated in later updates.
Here the roadplan of features is described with any upcoming/planned features. ETA's will not be provided, already implemented features will be ticked off. Only major features will be listed here, for further details on package development history, instead, refer to the NEWS file.
Note: list is subject to changes and is not necessarily definetive.
Clone the repository with
git clone https://github.com/Berghopper/GAPGOM.git.
Make a new package project with an existing directory using the latest Rstudio.
After having the project loaded, first make sure you have all the packages from the DESCRIPTION file installed (both Imports and Suggests packages).
methods are all standard R packages and packages that reside on cran are:
reshape2. The rest of the packages can be found on Bioconductor.
After installing all dependencies, the project can be built/compiled with Rstudio, click on the
build tab >
more and choose your option. Building might also require additional packages such as
devtools. For building vignettes, you can use the
devtools::build_vignettes() command. The built package should be able to be loaded with regular
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