get_candidate_module {ProgModule}

Get candidate module.

Description

The function 'get_candidate_module' is used to search candidate module of each local network using greedy algorithm.

Usage

get_candidate_module(
  local_network,
  network,
  freq_matrix,
  sur,
  seed,
  max.size,
  rate
)

Arguments

local_network

The local networks,generated by 'get_local_network'.

network

The maximum connected subnet,extracted by mapping all mutated genes to the PPI network.

freq_matrix

The mutations matrix,generated by 'get_mut_status'.

sur

A nx2 data frame of samples' survival data,the first line is samples' survival event and the second line is samples' overall survival.

seed

The canonical drivers from NCG database, which use as the starting node of the greedy algorithm.

max.size

The maximum size of the module,default is 200.

rate

The rate of increase in score,default is 0.05.

Value

candidate module.

Examples

#load the data
data(local_network)
data(mut_status)
data(subnet)
canonical_drivers<-system.file("extdata","canonical_drivers.txt",package = "ProgModule")
seed_gene<-read.table(canonical_drivers,header=FALSE)
sur<-system.file("extdata","sur.csv",package = "ProgModule")
sur<-read.delim(sur,sep=",",header=TRUE,row.names=1)
#perform the function `get_candidate_module`.
candidatemodule.example<-get_candidate_module(local_network=local_network,network=subnet,
freq_matrix=mut_status,sur=sur,seed=seed_gene[,1],max.size=200,rate=0.05)