otter: Run OTTER in R

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Run OTTER in R

Description

Description: OTTER infers gene regulatory networks using TF DNA binding motif (W), TF PPI (P), and gene coexpression (C) through minimzing the following objective: min f(W) with f(W) = (1-lambda)*||WW' - P||^2 + lambda*||W'W - C||^2 + (gamma/2)*||W||^2

Usage

otter(W, P, C, lambda = 0.035, gamma = 0.335, Iter = 60, eta = 1e-05, bexp = 1)

Arguments

W	: TF-gene regulatory network based on TF motifs as a matrix of size (t,g), g=number of genes, t=number of TFs
P	: TF-TF protein interaction network as a matrix of size (t,t)
C	: gene coexpression as a matrix of size (g,g)
lambda	: tuning parameter in [0,1] (higher gives more weight to C)
gamma	: regularization parameter
Iter	: number of iterations of the algorithm
eta	: learning rate
bexp	: exponent influencing learning rate (higher means smaller) Outputs:

Details

Inputs:

Value

W : Predicted TF-gene complete regulatory network as an adjacency matrix of size (t,g).

Examples

W=matrix(rexp(100, rate=.1), ncol=10)
C=matrix(rexp(100, rate=.1), ncol=10)
P=matrix(rexp(100, rate=.1), ncol=10)

# Run OTTER algorithm
W <- otter(W, P, C)
 

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.