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Analysis of allele-specific methylation (and changes in it)
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FDR_control
data
real_data_analysis
score_evaluation update figures for paper Sep 26, 2019
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README.md
allele_specificity_paper.Rproj

README.md

DAMEfinder: A method to detect allele-specific differential methylation

Code and data analysis

This repository contains the code for the following paper:

  • S Orjuela, D Machlab, M Menigatti, G Marra, MD Robinson: DAMEfinder: A method to detect allele-specific differential methylation. (in prep.)

The structure of this repository is as follows:

  • data/ Metadata from samples analyzed and R objects (.RData files).
  • real_data_analysis/ Contains R scripts ans bash scripts with to analyze raw BS-seq FASTQ files from two datasets: Monocyte datasets and CRC dataset.
  • score_evaluation/ R scripts to evaluate the ASMtuple score.
  • FDR_control/ R scripts to generate simulations and evaluate the FDR control in the DAME detection.
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