Methylation signature analysis with independent component analysis.
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.
Install from the GitHub repository using devtools:
install.packages("devtools")
library(devtools)
install_github("FunGeST/MethICA")
For the extraction of methylation signature MethICA requires one mandatory input file -- a methylation level 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 CpG annotation file describing the epigenetic context of CpG sites, and a sample annotation providing any relevant information about the samples.
The input files should have the following format. Example input files are provided with the package.
1]. bval : methylation level data
Rownames: CpG IDsColnames: Sample IDs
Optional: (the header is required, but the order of the columns can change)
2]. CpG annotation:
TargetID: CpG ID. Any alphanumeric string.state: Chromatin state (active/inactive)domain: Chromatin domain (ROADMAP nomenclature)CpG_context: Methylation domain (HMD/PMD/LMR/UMR)cgi_feature: CpG-island based feature (Island, Shore, Shelf, out of cgi)gene_feature: Gene-based feature (Body, TSS500, out)gene_name: Gene namedecile: Replication timing decile (1: early --> 10: late)CHROM: Chromosome. Between chr1 and chr22 or the chrX or chrY ('chr' prefix required).MAPINFO: CpG position (CHROM and MAPINFO are only required to annotate the CpG table with epigenomic features using chromatin.feature function)
3]. annot_data: sample annotation data
Sample: Sample identifier. Any alphanumeric string.- add in column the annotations you are interested in testing
- The RUNNING_METHICA_EXAMPLE folder contains an example R script (MethICA_example_script.R) for a typical MethICA analysis.
Test data can be downloaded here: https://drive.google.com/drive/folders/1BTQOhvI_qQou1CD94N_TCV_TEbcBC671?usp=sharing
Please try!
- Introduction to MethICA provides a comprehensive example of the MethICA workflow with detailed explanations of each function.
Copyright (C) 2020 Léa Meunier
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.
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.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.