WSHScripts

Introduction

This repository contains all scripts relevant to reproduce the results in Scherer M., et al., Quantitative comparison of within-sample heterogeneity scores for DNA methylation data , Nucleic Acids Research, 2020, 10.1093/nar/gkaa120. These scores are qFDRP, FDRP, PDR, MHL, Epipolymorphism and Entropy. The repository contains the following folders:

misc

Contains scripts that are used in various occassions by the pipelines, for instance to add a methylation call string (similar to bismark) to a bam file.

plotting_scripts

Contains R scripts needed to reproduce the plots/analysis from the publication, both for synthetic and biological data.

real_world_applications

Contains the scripts for the calculation on the two RRBS data sets, i.e. the healthy blood data set and the Ewing sarcoma cancer example.

scores

Contains the implementation of the scores.

simulation

Contains the pipelines used to compare the WSH scores on synthetic data.

License

Please note that the GNU GPL-3 license applies to all of the code in this repository with the exception of the MHL scripts, which are located in scores/MHL and whose license/permission to use is stated in the source files.