ssMutPA (version 0.1.2)

get_RWR_ES: Calculate the single-sample mutation-based pathway enrichment score.

Description

The function `get_RWR_ES` is used to calculate the single-sample mutation-based pathway enrichment score. Using somatic mutation data,PPI network and pathway data.

Usage

get_RWR_ES(
  mut_status,
  min_sample = 0,
  max_sample = dim(mut_status)[1],
  net_data,
  pathway_data,
  r = 0.7,
  Numcore = 2,
  BC_Num = length(V(net_data)$name),
  cut_point = 0
)

Value

A single-sample mutation-based pathway enrichment score profiles, where each element represents the enrichment score of a pathway in a sample.

Arguments

mut_status

A binary mutation matrix.The file can be generated by the function `get_mut_status`.

min_sample

The minimum number of mutated genes contained in a sample,default to 0.

max_sample

The maximum number of mutated genes contained in a sample.

net_data

A list of the PPI network information, including nodes and edges.

pathway_data

A data frame containing the pathways and their corresponding genes. The first column is the names of pathways and the second column is the genes included in the pathways.

r

A numeric value between 0 and 1. r is a certain probability of continuing the random walk or restarting from the restart set. Default to 0.7.

Numcore

The number of threads when running programs with multiple threads,default to 2 .

BC_Num

Number of background genes required to calculate seed node weight.

cut_point

The threshold of indicator function .

Examples

#load the data
data(mut_status)
net_path <- system.file("extdata","ppi_network.Rdata",package = "ssMutPA")
load(net_path)
pathway_path<-system.file("extdata","kegg_323_gmt.Rdata",package = "ssMutPA")
load(pathway_path)
samp_name<-c("TCGA-06-0881-01A","TCGA-76-4934-01A")
examp_data<-mut_status[,samp_name]
#perform the function `get_RWR_ES`.
Path_ES<-get_RWR_ES(examp_data,net_data=ppi_network,pathway_data=kegg_323_gmt,BC_Num=12436)