EpiTraceAge

Main function for age estimation.

Input:

  • mat: a count matrix for scATAC/ATAC data, usually built with ArchR, SnapATAC or Signac etc. Row = peaks and col = cells. Specifically, each row (peak) is overlapping with ClockDML.

  • normalization_method: normalization method used in EpiTraceAge computation, choose between ‘randomized’, ‘census’, and ‘blank’.

  • ncores: number of cores used in parallel processing

  • size: depreciated parameter

  • subsamplesize: subsample cell number, default to 2000.

  • select_minimal_percentage: selecting peaks covered in > this fraction of cells to compute dispersion. Default to 0.05. Suggest not to change unless necessary.

  • select_size_of_dispersion: numbers of peaks selected for computing the similarity matrix, ranked by dispersion. Default to 3000. Suggest not to change unless necessary.

Output: a data frame with columns: EpiTrace = epitrace age, Accessible_Loci = total accessibility on clock regions, cells=used cells.