transformation.matrix: Bi-partite network analysis tools

In QuackenbushLab/MONSTER: Modeling Network State Transitions from Expression and Regulatory data (MONSTER)

Description

This function analyzes a bi-partite network.

Usage

transformation.matrix(network.1, network.2, by.tfs = TRUE,
  standardize = FALSE, remove.diagonal = TRUE, method = "ols")

Arguments

network.1	starting network, a genes by transcription factors data.frame with scores for the existence of edges between
network.2	final network, a genes by transcription factors data.frame with scores for the existence of edges between
by.tfs	logical indicating a transcription factor based transformation. If false, gives gene by gene transformation matrix
standardize	logical indicating whether to standardize the rows and columns
remove.diagonal	logical for returning a result containing 0s across the diagonal
method	character specifying which algorithm to use, default='ols'

Value

matrix object corresponding to transition matrix

Examples

data(yeast)
cc.net.1 <- monsterNI(yeast$motif,yeast$exp.cc[1:1000,1:20])
cc.net.2 <- monsterNI(yeast$motif,yeast$exp.cc[1:1000,31:50])
transformation.matrix(cc.net.1, cc.net.2)

QuackenbushLab/MONSTER documentation built on Oct. 22, 2020, 8:07 a.m.