Estimate "background" accessibility rate from a reference cell‐type peak list

Estimate "background" accessibility rate from a reference cell‐type peak list

get_average_bg(count_matrix, cell_type_cells, cell_type_peaks)

Arguments

count_matrix

A peaks-by-cells matrix (dgCMatrix or dense).

cell_type_cells

list of cells of the specific cell type

cell_type_peaks

Path to a BED file of that cell type’s peaks (three cols: chr, start, end).

Value

A single numeric: the estimated baseline accessibility probability.

Examples

if (FALSE) { # \dontrun{
get_average_bg(cm, "CD8", "cd8_peaks.bed")
} # }