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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

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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