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mND score

mND.Rd

Calculation of mND score

Usage

mND(Xs = NULL, ind_adj = NULL, k = 3, BPPARAM = NULL, min.norm.val = 0)

Arguments

Xs

a matrix or list of matrices (if X0 was permuted, where the first element of the list is the one obtained with real data) with network diffusion scores, see 'ND' function

ind_adj

list; index of neighbours obtained from adjacency matrix, see 'neighbour_index' function

k

numeric; number of top k first neighbors

BPPARAM

optional BiocParallelParam instance determining the parallel back-end to be used during evaluation. If NULL, parallel evaluation is disabled using SerialParam(). See ?bplapply.

min.norm.val

normalized ND values below this value will be set to 0; this is useful to denoise the steady state of ND and focus only on the highest scores

Value

list with:

  • mND: mND score

  • t: sum of top k neighbours

If data were permuted (therefore Xs is a list), the output list described above will be reported for each permutation of Xs.