Usage: Generate BEDGRAPH Files for Single Analysis - GarrettJenkinson/informME GitHub Wiki

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 --ESI flag passed): entropic sensitivity indices

• MSI-PHENO.bed (if --MSI flag passed): methylation sensitivity indices

• TURN-PHENO.bed (if --MC flag passed): turnover ratios

• CAP-PHENO.bed (if --MC flag passed): channel capacities

• RDE-PHENO.bed (if --MC flag passed): 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                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 the BED files that include chr1 through chr10 for phenotype normal:
    	singleMethAnalysisToBed.sh --min_chr 1 --max_chr 10 normal
    * Generating the BED files including MC, ESI, and MSI quantities for phenotype normal:
    	singleMethAnalysisToBed.sh --MC --ESI --MSI normal

Output:
    BED files

Dependancies:
    MATLAB

Upstream:
    mergeSingleMethAnalysis.sh 

Authors:
    Garrett Jenkinson <[email protected]>
    Jordi Abante <[email protected]>