CreateWalkMatrix: Create Walk Matrix

In bozdaglab/PhenoGeneRanker: PhenoGeneRanker: A gene and phenotype prioritization tool

Description

Generates a Walk Matrix (Transition Matrix) from Gene and Phenotype networks for RWR.

Usage

CreateWalkMatrix(
  inputFileName,
  numCores = 1,
  delta = 0.5,
  zeta = 0.5,
  lambda = 0.5
)

Arguments

inputFileName	The name of the text file that contains the names of gene and phenotype network files. For more information on the file formatting, please refer the vignette.
numCores	This is the number of cores used for parallel processing.
delta	This is the probability of jumping between gene layers. High delta means RWR is high likely to jump to other layers in gene multiplex network. It has a default value of 0.5.
zeta	This is the probability of jumping between phenotype layers. High zeta means RWR is high likely to jump to other layers in phenotype multiplex network. It has a default value of 0.5.
lambda	This is the probability of jumping between gene and phenotype multiplex networks. High lambda means RWR is more likely to exploit the bipartite relation. It has a default value of 0.5.

Value

This returns a list containing the walk matrix, a sorted list of gene ids, a sorted list of phenotype ids, the connectivity degree of the genes, the connectivity degree of the phenotypes, the number of gene layers, the number of phenotype layers, the number of genes and the number of phenotypes in the final complex network.

Examples

wm <- CreateWalkMatrix('input_file.txt')
customWm <- CreateWalkMatrix('input_file.txt', numCores=1, delta=0.7, zeta=0.7, lambda=0.7)

bozdaglab/PhenoGeneRanker documentation built on March 11, 2021, 5:37 a.m.