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

In ssMutPA: Single-Sample Mutation-Based Pathway Analysis

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
)

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 .

Value

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

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)

ssMutPA documentation built on Oct. 16, 2024, 1:06 a.m.