mND: mND score

In emosca-cnr/mND: Gene relevance based on multiple evidences in complex networks

mND score

Description

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.

emosca-cnr/mND documentation built on April 11, 2024, 12:49 p.m.