Get region (peak) by cell type matrix and per cell capturing rate

For a snATAC-seq (binary) dataset, compute the peak-specific open probability and cell-specific capturing rates

Usage

get_r_by_ct_mat_pq(
  cell_type_set,
  r_by_c,
  cell_type_labels,
  n_features_per_cell = nrow(r_by_c),
  p_acc = 5e-04,
  q_acc = 5e-04,
  n_max_iter = 800,
  verbose = TRUE
)

Arguments

cell_type_set

A vector containing all cell types

r_by_c

Input region (peak) by cell matrix. Nonzero entries are binarized internally.

cell_type_labels

A vector containing cell type labels

n_features_per_cell

The number of features in the matrix, defaulting to nrow(r_by_c). If supplied, it must match that value.

p_acc

The accuracy of p, default specified as 0.0005

q_acc

The accuracy of q, default specified as 0.0005

n_max_iter

The maximum iteration, default = 800

verbose

Whether to output information on processing status

Value

A list with two elements,

• p_by_t Peak by cell type matrix, each element represents the open probability of the peak in the corresponding cell type

• q_vec A vector of cell-specific capturing rate