EpiTrace_prepare_object

Input:

  • peakSet: a prepared “peak set” GRanges object.

  • matrix: a prepared read count matrix.

  • celltype: optional annotation for cell types. Usually not required.

  • sep_string: used to split the peak names. Usually as c(“:”,”_”,”-“).

  • clock_gr_list: GRange list for reference clock-like loci. A list.

  • non_standard_clock: set to T when you need to use non-human, non-ClockDML genomic loci as reference.

  • qualnum: minimal peaks that a cell/sample should have.

  • remove_peaks_number: minimal number of cells that a peak should be positive on.

  • ref_genome: when it is set to “hg19” or “hg38”, the program can automatically use the ClockDML from package. Otherwise, you should provide your own reference clock-like loci.

  • run_reduction: set to F if you would not like Signac dimensionality reduction to run.

  • fn.k.param: KNN cluster parameter for Signac.

  • lsi_dim: LSI dimensions to be used in Signac dimensionality reduction.

  • min.cutoff: minimal cutoff for Signac::FindTopFeatures. Used when you ask the program to run dimensionality reduction.

Output: an “epitrace” Seurat object to be used in downstream analysis.

NOTE Do not use this function unless you intend to do the analysis step-by-step manually. The iterative updating function does not need object preparation at initial. The function is more internal and not recommended for application use. For application, we suggest directly using EpiTraceAge_Convergence.