get_final_module {ProgModule}

Get final module.

Description

The function 'get_final_module' is used to identify the final module.

Usage

get_final_module(
  index,
  edge,
  mut_status,
  sur,
  seed,
  cutoff = 0.05,
  max.size.local = 500,
  max.size.candidate = 200,
  rate = 0.05,
  perm = 1000
)

Arguments

index

A index file of PPI networks,downloaded from http://compbio-research.cs.brown.edu/pancancer/hotnet2/.

edge

The edge lists of PPI networks,downloaded from http://compbio-research.cs.brown.edu/pancancer/hotnet2/.

mut_status

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.

cutoff

The perturbed p-value cutoff point,default is 0.05.

max.size.local

The size of maximum connected local network,default is 500.

max.size.candidate

The maximum size of the candidate module,default is 200.

rate

The rate of increase in score,default is 0.05.

perm

The perturbation number,default is 1000.

Value

The final module.

Examples

#load the data
indexdata<-system.file("extdata","hint+hi2012_index_file.txt",package="ProgModule")
index<-read.table(indexdata,sep="\t",header=FALSE)
edgedata<-system.file("extdata","hint+hi2012_edge_file.txt",package="ProgModule")
edge<-read.table(edgedata,sep="\t",header=FALSE)
data(mut_status)
sur<-system.file("extdata","sur.csv",package ="ProgModule")
sur<-read.delim(sur,sep=",",header=TRUE,row.names=1)
canonical_drivers<-system.file("extdata","canonical_drivers.txt",package="ProgModule")
seed_gene<-read.table(canonical_drivers,header=FALSE)
#perform the function `get_final_module`.
finalmodule.example<-get_final_module(index,edge,mut_status,sur,seed=seed_gene,
cutoff=0.05,max.size.local=500,max.size.candidate=200,rate=0.05,perm=100)