Gene classification

Gene classification: genes are classified in every layer

Usage

classification(mND, X0, Hl, top = NULL, alpha = NULL)

Arguments

mND

mND scores; if data were permuted use the output of 'signif_assess' function, otherwise output of 'mND' function

X0

matrix; initial score matrix X0, in which each column (layer) represents a score vector over all vertices of G

Hl

list; defined by the user, composed of high scoring genes names in each layer of X0.

top

array; number of genes with the highest neighbourhoods to define the gene set Nl (see below); 1 number for each layer.

alpha

array; significance level on the empirical p-value to define the gene set Nl (see below); 1 number for each layer.

Value

list with:

• gene_class: data.frame with classifications of each gene in every layers. The possible classification are: M (Module); L (Linker); I (Isolated); NS (Not Significant);

• occ_labels: occurrence of the different labels (M; L; I; NS) for each gene across layers.

Details

The gene set Nl contains the genes with the highest neighbourhoods in layer l. If both 'top' and 'alpha' are provided, a maximum of top genes with p < alpha will be considered.