RunEpiTraceAge

Input:

• epitrace_object: an prepared EpiTrace object.

• parallel: set to T if you want multicore support. Requires parallel package.

• ncores: threads used in parallel computation.

• subsamplesize: cell number (randomly sampled) to be used in parallel computation.

• normalization_method: choose between “randomized”, “census”, and “blank”. Default to “randomized”.

• select_minimal_percentage: minimal cell fraction that showing coverage on the selected peak. Default to 0.05.

• select_size_of_dispersion: number of peaks selected for computing the similarity matrix, ranked by dispersion.

Output: an epitrace_object with cell ages determined. This is a Seurat object. In the object, most important results are EpiTraceAge_xxxx. EpiTrace result from a particular (xxxx) reference clock-like loci. By default it runs for individual reference clock-like loci in clock_gr_list.

• EpiTraceAge_Mitosis: the age inferred by ‘Mitosis’ clock-like loci.

• EpiTraceAge_Chronology: the age inferred by ‘Chronology’ clock-like loci.

• EpiTraceAge_All: the age inferred by combining both ‘Mitosis’ and ‘Chronology’ loci.

The function is more internal and not recommended for application use. For application, we suggest directly using EpiTraceAge_Convergence.