Calculate the threshold for calling peaks — get_quantile_cov

Threshold is calculated by taking the maximum between the quantile_thresh quantile of the ATAC marginal and min_umis.

Usage

get_quantile_cov_thresh(
  marginal_track,
  quantile_thresh,
  min_umis,
  window_size,
  genome = NULL,
  seed = 60427
)

marginal_track: Name of the 'misha' track to call peaks from. You can create it using import_atac_marginal.
quantile_thresh: Quantile threshold to use.
min_umis: Minimum number of UMIs to use.
window_size: size of the window to use for the calculation of the quantile.
genome: Genome name, such as 'hg19' or 'mm10'. If NULL - the current genome is used.
seed: random seed for reproducibility (misha::gquantiles sometimes samples the data.

The number of UMIs to use for calling peaks.

if (FALSE) {
get_quantile_cov_thresh("pbmc_atac.marginal", quantile_thresh = 0.9, min_umis = 8, genome = "hg38")
}