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Usage: Generate BEDGRAPH Files for Single Analysis

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GarrettJenkinson edited this page May 29, 2018 · 3 revisions

Command:

singleMethAnalysisToBed.sh [OPTIONS] -- PHENO

This function makes BED files from the methylation analysis results obtained after running informME_run.sh for a given phenotype PHENO. By default, the input file (analysis file) is expected to be located in INTERDIR/chr#/PHENO_analysis.mat. In addition, the output files are stored in FINALDIR and have the following names and content:

  • MML-PHENO.bed: mean methylation levels

  • NME-PHENO.bed: normalized methylation entropy

  • METH-PHENO.bed: methylation-based classification (non-variable)

  • VAR-PHENO.bed: methylation-based classification (variable)

  • ENTR-PHENO.bed: entropy-based classification

  • ESI-PHENO.bed (if ESIflag = 1): entropic sensitivity indices

  • TURN-PHENO.bed (if MCflag = 1): turnover ratios

  • CAP-PHENO.bed (if MCflag = 1): channel capacities

  • RDE-PHENO.bed (if MCflag = 1): relative dissipated energies

NOTE: Here is the full help file for singleMethAnalysisToBed.sh:

Description:
    This function makes BED files from the methylation analysis results obtained after 
    running informME_run.sh for a given phenotype. By default, the input file (analysis 
    file) is expected to be located in INTERDIR, whereas the output files are stored 
    in FINALDIR. 

Usage:
    singleMethAnalysisToBed.sh [OPTIONS] -- PHENO

Mandatory argument:
    o PHENO: prefix of the methylation analysis file (name of phenotype)

Options:
    -h|--help           help
    -r|--refdir         directory of reference genome (default: $REFGENEDIR)
    -a|--analdir        analysis directory (default: $REFGENEDIR)
    -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                computation of information theoretic quantities (default: 0)
    --ESI               computation of entropic sensivity index (ESI) (default: 0)
    -l|--MATLICENSE     path to MATLAB's license

Example:
    * Generating the BED files that include chr1 through chr22 for phenotype normal:
    	singleMethAnalysisToBed.sh --min_chr 1 --max_chr 22 -- normal

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.

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