build_sim_net: Build the gene similarity network from annoations

In wulingyun/CopTea: Combinatorial OPTimization based Enrichment Analysis

Description

Build the gene similarity network from the core sets matrix by using Cohen's kappa statistic.

Usage

build_sim_net(core.sets, kappa.threshold = 0.9)

Arguments

core.sets	Logical matrix indicated the core genes associated with specific functions or pathways. The rows correspond to genes, while the columns represent the functions or pathways.
kappa.threshold	The threshold to establish a link between two genes if their kappa score is larger than the threshold.

Details

This function build the gene similarity network from the gene annotations, which is given by a core sets matrix. The Cohen's kappa statistic is used to compute the similarity between two genes.

Value

This function returns a sparse adjacent matrix of the gene similarity network.

wulingyun/CopTea documentation built on Dec. 4, 2019, 2:59 p.m.