k_clique: k-clique algorithm

In hanjunwei-lab/crmSubpathway: Identify cancer-related metabolic subpathways

Description

Mining metabolic subpathways through k-clique algorithm.

Usage

k_clique(file.path = "", file.names = "", K = 4)

Arguments

file.path	Path of KGML files (XML format).
file.names	A character vector of names of KGML files.
K	An integer. A distance similarity parameter (default: 4).

Details

k_clique

In this method, we convert the each metabolic pathways in the KEGG database into an undirected network diagram by connecting two genes (enzymes) into an edge if there is a common compound in their corresponding reactions. Based on the distance similarity between genes, we use the K-clique method in social network analysis to mine subpathways and the distance between all genes is no exceeding K is determined as the metabolic subpathway.At the same time, our method can also be applied to other non-metabolic pathways of KEGG database.

Examples

library(graph);
library(RBGL);
library(igraph);
library(XML);
file.path<-paste(system.file(package="crmSubpathway"),"/extdata/",sep="")
file.names<-c("hsa00010.xml","hsa00020.xml")
spwlist<-k_clique(file.path,file.names)

hanjunwei-lab/crmSubpathway documentation built on Jan. 26, 2021, 8:50 a.m.