get_P: get_P

In ShandongUniversityZhanglab/DriverRWH: DriverRWH: Discovering Cancer Driver Genes by Random Walk on a Gene Mutation Hypergraph

get_P

Description

get_P uses the mutation data and the vertex weight of the hypergraph to calculate the transition possibility matrix output of get_P is the transition possibility matrix of the hypergraph

Usage

get_P(Mutation, vertex_W)

Arguments

Mutation	the mutation data, rows represent genes and columns represent samples
vertex_W	the vertex weight of the hypergraph

Examples

###the vertex weight of the hypergraph is calculated by get_vertex_W(Mutation,graph)
###and some relevant data should be calculated

###the example mutation data is a Lung Squamous Cell Carcinoma Dataset from TCGA
###We will show how to get the transition possibility matrix of the hypergraph

library(DriverRWH)

#load the mutation data
data(luscExampleMutation)

#load the network data
data(HumanNet)

#get the graph from HumanNet
graph=graph.data.frame(HumanNet)

#get the vertex weight of the hypergraph
W=get_vertex_W(Mutation=luscExampleMutation,graph=graph)

#get the transition possibility matrix P
P=get_P(Mutation=luscExampleMutation,vertex_W=W)

ShandongUniversityZhanglab/DriverRWH documentation built on May 10, 2022, 2:47 a.m.