Create an McPeaks object from McTracks object

Create an McPeaks object from an McTracks object by extracting the atac data from the tracks at the peaks.

Usage

mct_to_mcatac(
  mct,
  peaks,
  metacells = NULL,
  metadata = NULL,
  mc_size_eps_q = 0.1,
  parallel = getOption("mcatac.parallel")
)

mct: an McTracks object
peaks: a data frame with the peak intervals (chrom, start, end) and a column called "peak_name"
metacells: names of metacells to include. Default: all metacells.
metadata: (optional) per-metacell metadata. A data frame with a column called 'metacell' and additional metacell annotations.
mc_size_eps_q: (optional) quantile of MC size (in UMIs) to scale the number of UMIs per metacell. \(egc_ij\) would then be the fraction of peak i in metacell j multiplied by the mc_size_eps_q quantile of metacell sizes.

a McPeaks object

if (FALSE) {
atac_mc <- mct_to_mcatac(mct, peaks)
}