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README.html
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<body>
<h1 id="toc_0">MethICA</h1>
<p>Methylation signature analysis with independent component analysis.</p>
<p>Description: apply independent component analysis (ICA) to methylation data to extract epigenetic signatures and perform downstream analyses and representations to interpret the biological meaning of methylation components.</p>
<h2 id="toc_1">Installation</h2>
<h1 id="toc_2"></h1>
<p>Install from the GitHub repository using devtools:</p>
<p>install.packages("devtools")
library(devtools)
devtools::install_github("FunGeST/MethICA")</p>
<h2 id="toc_3">Input files</h2>
<h1 id="toc_4"></h1>
<p>For the extraction of methylation signature <em>MethICA</em> requires one mandatory input file -- a <strong>methylation level</strong> file (bval) describing methylation levels of individual CpG sites or genomic regions (row) in each sample (column). Two additional files are needed for the interpretation of methylation components: a <strong>CpG annotation</strong> file describing the epigenetic context of CpG sites, and a <strong>sample annotation</strong> providing any relevant information about the samples.</p>
<p><strong>The input files should have the following format. Example input files are provided with the package.</strong></p>
<p><code>1]. bval</code>: <strong>methylation level data</strong></p>
<ul>
<li><code>Rownames</code> : CpG IDs</li>
<li><code>Colnames</code> : Sample IDs</li>
</ul>
<p><strong>Optional: (the header is required, but the order of the columns can change)</strong></p>
<p><code>2]. CpG annotation</code>:</p>
<ul>
<li><code>TargetID</code> : CpG ID. Any alphanumeric string.</li>
<li><code>state</code> : Chromatin state (active/inactive)</li>
<li><code>domain</code> : Chromatin domain (ROADMAP nomenclature)</li>
<li><code>CpG_context</code> : Methylation domain (HMD/PMD/LMR/UMR)</li>
<li><code>cgi_feature</code> : CpG-island based feature (Island, Shore, Shelf, out of cgi)</li>
<li><code>gene_feature</code> : Gene-based feature (Body, TSS500, out)</li>
<li><code>gene_name</code> : Gene name</li>
<li><code>decile</code> : Replication timing decile (1: early --> 10: late)</li>
<li><code>CHROM</code> : Chromosome. Between chr1 and chr22 or the chrX or chrY ('chr' prefix required).</li>
<li><code>MAPINFO</code> : CpG position (CHROM and MAPINFO are only required to annotate the CpG table with epigenomic features using chromatin.feature function)</li>
</ul>
<p><code>3]. annot_data</code>: <strong>sample annotation data</strong></p>
<ul>
<li><code>Sample</code>: Sample identifier. Any alphanumeric string.</li>
<li>add in column the annotations you are interested in testing</li>
</ul>
<h2 id="toc_5">Running MethICA</h2>
<h1 id="toc_6"></h1>
<ul>
<li>The <a href="https://github.com/FunGeST/MethICA">RUNNING_METHICA_EXAMPLE</a> folder contains an example dataset and an R script of a typical MethICA analysis. Please try!</br></li>
<li>[<em>Introduction to MethICA</em>] provides a comprehensive example of the MethICA workflow with detailed explanations of each function.</br> </li>
</ul>
<h2 id="toc_7">License</h2>
<h1 id="toc_8"></h1>
<p>Copyright (C) 2020 Léa Meunier</p>
<p>MethICA is a free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.</p>
<p>This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.</p>
<p>You should have received a copy of the GNU General Public License
along with this program. If not, see <a href="http://www.gnu.org/licenses/">http://www.gnu.org/licenses/</a>.</p>
</body>
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