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Usage: Generate BEDGRAPH Files for Differential Analysis
Command:
diffMethAnalysisToBed.sh [OPTIONS] PHENO1 PHENO2
This function makes BED files for the differential methylation analysis results obtained after running informME_run.sh for two given phenotypes PHENO1 and PHENO2. By default, the input files (both analysis files) are expected to be located in INTERDIR/chr#/PHENO1_analysis.mat and INTERDIR/chr#/PHENO2_analysis.mat respectively. In addition, the output files are stored in FINALDIR and have the following names and content:
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dMML-PHENO1-VS-PHENO2.bed: differences in mean methylation levels
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DMU-PHENO1-VS-PHENO2.bed: differential mean-based classification
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dNME-PHENO1-VS-PHENO2.bed: differences in normalized methylation entropies
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DEU-PHENO1-VS-PHENO2.bed: differential entropy-based classification
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JSD-PHENO1-VS-PHENO2.bed: Jensen-Shannon distances
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dESI-PHENO1-VS-PHENO2.bed (if --ESI flag passed): differences in entropic sensitivity indices
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dMSI-PHENO1-VS-PHENO2.bed (if --MSI flag passed): differences in methylation sensitivity indices
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dCAP-PHENO1-VS-PHENO2.bed (if --MC flag passed): differences in channel capacities
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dRDE-PHENO1-VS-PHENO2.bed (if --MC flag passed): differences in relative dissipated energies
NOTE: Here is the full help file for diffMethAnalysisToBed.sh
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Description:
This function makes BED files from the differential methylation analysis results obtained
after running informME_run.sh for two given phenotypes. By default, the input files
(both analysis files) are expected to be located in INTERDIR, whereas the output files
are stored in FINALDIR.
Usage:
diffMethAnalysisToBed.sh [OPTIONS] PHENO1 PHENO2
Mandatory arguments:
o PHENO1: prefix of the methylation analysis file 1 (name of phenotype 1)
o PHENO2: prefix of the methylation analysis file 2 (name of phenotype 2)
Options:
-h|--help help
-r|--refdir reference genome directory (default: $REFGENEDIR)
-a1|--analdir_1 analysis directory for phenotype 1 (default: $INTERDIR)
-a2|--analdir_2 analysis directory for phenotype 2 (default: $INTERDIR)
-d|--outdir output directory (default: $FINALDIR)
-t|--threshold threshold used in methylation-based classification (default: 0.4)
--min_chr minimum chromosome to be included in BED file (default: 1)
--max_chr maximum chromosome to be included in BED file (default: 22)
--MC do computation of information theoretic quantities
--ESI do computation of entropic sensivity index (ESI)
--MSI do computation of methylation sensivity index (MSI)
-l|--MATLICENSE path to MATLAB's license
Example:
* Generating BED files for differential analysis between phenotype_1 and phenotype_2
between chr1-10:
diffMethAnalysisToBed.sh --min_chr 1 --max_chr 10 phenotype_1 phenotype_2
* Generating BED files including ESI, MSI, and MC computations for differential analysis
between phenotype_1 and phenotype_2:
diffMethAnalysisToBed.sh --ESI --MSI --MC phenotype_1 phenotype_2
Output:
BED files
Dependancies:
MATLAB
Upstream:
mergeSingleMethAnalysis.sh
Authors:
Garrett Jenkinson <[email protected]>
Jordi Abante <[email protected]>
If you use informME, please cite:
[1] Jenkinson, G., Pujadas, E., Goutsias, J., and Feinberg, A.P. (2017), Potential energy landscapes identify the information-theoretic nature of the epigenome, Nature Genetics, 49: 719-729.
[2] Jenkinson, G., Abante, J., Feinberg, A.P., and Goutsias, J. (2018), An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data, BMC Bioinformatics, 19:87, https://doi.org/10.1186/s12859-018-2086-5.
[3] Jenkinson, G., Abante, J., Koldobskiy, M., Feinberg, A.P., and Goutsias, J. (2019), Ranking genomic features using an information-theoretic measure of epigenetic discordance, BMC Bioinformatics, 20:175, https://doi.org/10.1186/s12859-019-2777-6.
- Home
- Software Overview
- Dependencies
- Installing InformME
- Directory Structure
- Usage
- Reference Genome Analysis
- Methylation Data Matrix Generation
- Model Estimation & Analysis
- Generate BEDGRAPH Files for Single Analysis
- Generate BEDGRAPH Files for Differential Analysis
- Postprocessing: BEDGRAPH to BW Conversion
- Postprocessing: DMR Detection
- Postprocessing: Gene Ranking
- Testing/Debugging Your Install
- FAQs
- Version History
- Licencing