Clock Reference Options

EpiTrace provides multiple reference clock-like loci sets for age estimation.

Available Clock Sets

Standard Clock Sets (included with the package)

Mitosis (616 regions) - Contains only hypermethylation sites - Shows strong positive correlation with mitotic age - Best for: Detecting recent cell divisions, identifying highly proliferative cells - Use when: Focus on mitosis-specific age estimation
Chronology (125,625 regions) - Contains clock-like DML/DMR from multiple studies - Excludes regions overlapping with Mitosis clock - Mix of hyper- and hypomethylation patterns - Best for: General age estimation across cell types - Use when: Balanced view of cellular aging
solo_WCGW (1,669,720 regions) - Solitary WCGW (WCGW = Ws/C/Gs) motifs in partially methylated domains - Contains only hypomethylation sites - Large number of regions (1.6M vs 616 for Mitosis) - Best for: Research on WCGW-specific patterns, comparative studies - Use when: Investigating hypomethylation-specific age signatures
AllClock (Mitosis + Chronology) - Combined set of Mitosis and Chronology clocks (126,241 regions) - Default when using standard clock with RunEpiTraceAge() - Best for: Most applications, comprehensive age estimation - Use when: Standard EpiTrace analysis

Which Clock Should You Use?

For Most Applications (Recommended)

Use AllClock (the default):

# Default: uses Mitosis + Chronology
obj <- EpiTrace_prepare_object(peakset, matrix, celltype,
                               clock_gr_list = clock_gr_list,
                               standard_clock = TRUE)
obj <- RunEpiTraceAge(obj)

For Mitosis-Specific Age Estimation

Use Mitosis clock only:

# Use only Mitosis clock
custom_clock <- list(MitosisClock = clock_gr_list[['Mitosis']])
obj <- EpiTrace_prepare_object(peakset, matrix, celltype,
                               clock_gr_list = custom_clock,
                               non_standard_clock = TRUE)

For Hypomethylation Studies

Use solo_WCGW clock:

# Use solo_WCGW for hypomethylation-focused analysis
custom_clock <- list(solo_WCGW = clock_gr_list[['solo_WCGW']])
obj <- EpiTrace_prepare_object(peakset, matrix, celltype,
                               clock_gr_list = custom_clock,
                               non_standard_clock = TRUE)

Why is solo_WCGW Not Used in Tutorials?

The tutorials use AllClock (Mitosis + Chronology) rather than solo_WCGW for several reasons:

Computational efficiency - solo_WCGW has 1.6M regions vs 616 for Mitosis - Processing time increases significantly with more regions - Most applications don’t need this granularity
Biological interpretation - Mitosis + Chronology provides a balanced view - Combines hyper- and hypomethylation patterns - Validated in multiple cell types and systems
Validation - AllClock (Mitosis + Chronology) is extensively validated - Shown to work well across different datasets - solo_WCGW is primarily for specialized research questions

When to Consider solo_WCGW

Use solo_WCGW if:

Studying WCGW motif-specific aging patterns
Investigating hypomethylation-driven age changes
Comparing hyper- vs hypomethylation age signatures
Working with model systems where WCGW patterns are prominent
Exploring age-associated chromatin changes in partially methylated domains

Example Comparative Analysis

# Compare different clock sets
clocks_to_compare <- list(
  Mitosis = clock_gr_list[['Mitosis']],
  Chronology = clock_gr_list[['Chronology']],
  solo_WCGW = clock_gr_list[['solo_WCGW']]
)

results <- list()
for (clock_name in names(clocks_to_compare)) {
  obj <- EpiTrace_prepare_object(peakset, matrix, celltype,
                                 clock_gr_list = list(clock = clocks_to_compare[[clock_name]]),
                                 non_standard_clock = TRUE)
  obj <- RunEpiTraceAge(obj)
  results[[clock_name]] <- obj$EpiTraceAge_clock
}

# Compare correlations
cor(results[['Mitosis']], results[['Chronology']])
cor(results[['Mitosis']], results[['solo_WCGW']])

References

For more details on clock set construction: * Xiao et al. (2024) Nature Biotechnology - Methods section * Yang et al. (2016) - Mitosis clock DML * Youn and Wang (2018) - Chronology clock DML * Zhou et al. (2018) - solo_WCGW in partially methylated domains