Calculation of permutation-adjusted network smoothing index

Usage

calc_adjND(
  X0 = NULL,
  W = NULL,
  eps = NULL,
  k = 99,
  BPPARAM = NULL,
  bin_type = "number",
  method = "simple",
  cut_par = 20,
  vertex_sets = NULL,
  ...
)

Arguments

X0: input matrix
W: symmetrically normalized adjacency matrix W = D^-1 A D^-1, see normalize_adj_mat function
eps: matrix of eps values; same columns of X0; see eval_eps().
k: number of permutations
BPPARAM: An optional BiocParallelParam instance determining the parallel back-end to be used during evaluation. If NULL, parallel evaluation is disabled using SerialParam(); See BiocParallel::bplapply()
bin_type: see NPATools::perm_vertices()
method: see NPATools::perm_vertices()
cut_par: see NPATools::perm_vertices()
vertex_sets: see NPATools::perm_vertices() network smoothing values (Xs)
...: additional arguments passed to NPATools::ND()

Value

list of data frames