Table 1.

General guidelines for WSH scores

Score	Concept	Strengths	Drawbacks	Application scenario
PDR	Locally disordered methylation	Detects DNAm erosion; CpG-wise score; Fast computation	Simulated heterogeneity not detected; Dependency on read length and CpG density	Addressing locally disordered DNA methylation in large cancer datasets
MHL	Methylation haplotypes	CpG-wise score; Robust to technical setup	Simulated heterogeneity not detected; Slow computation	Linking genetically detected haplotypes to DNA methylation haplotypes
Epipoly	Variance among the reads	Simulated heterogeneity detected; Robust to technical setup	no CpG-wise score; Few regions captured	Segmentation into highly and lowly variably methylated regions for large bisulfite sequencing datasets
Entropy	Variance among the reads	Simulated heterogeneity detected; Robust to technical setup	no CpG-wise score; Few regions captured	Segmentation into highly and lowly variably methylated regions for large bisulfite sequencing datasets
FDRP	Variance among the reads	Simulated heterogeneity detected CpG-wise score	Dependency on coverage, read length and CpG density; Rather slow computation	Linking CpG-wise methylation values to epigenetic heterogeneity in large bisulfite sequencing datasets
qFDRP	Variance among the reads	Simulated heterogeneity detected; Robust to technical setup; CpG-wise score	Rather slow computation	Linking CpG-wise methylation values to epigenetic heterogeneity in large bisulfite sequencing datasets