randomWalkByMatrixInv,matrix-method {netSmooth}R Documentation

Smooth data on graph by computing the closed-form steady state distribution of the random walk with restarts process.

Description

The closed-form solution is given by f_ss = (1 - alpha) * (I - alpha * A)^-1 * f_0 and is computed by matrix inversion in this function.

Usage

## S4 method for signature 'matrix'
randomWalkByMatrixInv(
  f0,
  adjMatrix,
  alpha,
  normalizeAdjMatrix = c("rows", "columns")
)

Arguments

f0

initial data matrix [NxM]

adjMatrix

adjacency matrix of graph to network smooth on will be column-normalized.

alpha

smoothing coefficient (1 - restart probability of random walk)

Value

network-smoothed gene expression


[Package netSmooth version 1.12.0 Index]