Return a mask matrix with differential cluster accessibility (DCA)

This function detects differential cluster accessibility (DCA) for each sub-tree of a given hclust object with hierarchical clustering of the metacells.
For each coordinate (column) in the matrix, the function computes the log fold change between the subtree and the rest of the tree, and returns a mask matrix indicating whether the fold change is above or below the threshold(s).
In order to avoid very long DCAs, the functions limits the size of a peak/trough to a fraction of all the metacells (sz_frac_for_peak).

Usage

mct_diff_access_on_hc(
  mat,
  hc,
  sz_frac_for_peak = 0.25,
  u_reg = 4,
  peak_lf_thresh1 = 1.2,
  peak_lf_thresh2 = 2,
  trough_lf_thresh1 = -1,
  trough_lf_thresh2 = -2
)

Arguments

mat

a matrix where rows are coordinates and columns are metacells

hc

an hclust object with the order of the metacells

sz_frac_for_peak

maximal fraction of metacells in a peak or trough. Default is 0.25.

u_reg

regularization factor

peak_lf_thresh1, peak_lf_thresh2, trough_lf_thresh1, trough_lf_thresh2

thresholds for the log fold change of the peaks and troughs

Value

a matrix the same dimensions of mat, with a mask of differential cluster accessibility (DCA). A value of 1 means the log fold change was above peak_lf_thresh1, and a value of 2 means the log fold change was above peak_lf_thresh2. The same with -1 and -2 for troughs.