transformation.matrix: Bi-partite network analysis tools

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

Description

This function analyzes a bi-partite network, such as a Transcription factor to gene network derived from the PANDA algorithm.

Usage

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

Arguments

by.tfs	logical indicating a transcription factor based transformation. If false, gives gene by gene transformation matrix
remove.diagonal	logical for returning a result containing 0s across the diagonal
method	character specifying which algorithm to use, default='kabsch'
net1	starting network, a genes by transcription factors data.frame with scores for the existence of edges between
net2	final network, a genes by transcription factors data.frame with scores for the existence of edges between

Value

matrix object corresponding to transition matrix

Examples

data(yeast)
cc.net <- monsterNI(yeast$motif,yeast$exp.cc)
sr.net <- monsterNI(yeast$motif,yeast$exp.sr)
transformation.matrix(cc.net, sr.net)

dschlauch/MONSTER documentation built on May 15, 2019, 2:57 p.m.