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

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:

• dMML-PHENO1-VS-PHENO2.bed: differences in mean methylation levels

• DMU-PHENO1-VS-PHENO2.bed: differential mean-based classification

• dNME-PHENO1-VS-PHENO2.bed: differences in normalized methylation entropies

• DEU-PHENO1-VS-PHENO2.bed: differential entropy-based classification

• JSD-PHENO1-VS-PHENO2.bed: Jensen-Shannon distances

• dESI-PHENO1-VS-PHENO2.bed (if --ESI flag passed): differences in entropic sensitivity indices

• dMSI-PHENO1-VS-PHENO2.bed (if --MSI flag passed): differences in methylation sensitivity indices

• dCAP-PHENO1-VS-PHENO2.bed (if --MC flag passed): differences in channel capacities

• dRDE-PHENO1-VS-PHENO2.bed (if --MC flag passed): differences in relative dissipated energies

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

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]>