monsterTransformationMatrix: Bi-partite network analysis tools

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

Bi-partite network analysis tools

Description

This function analyzes a bi-partite network.

Usage

monsterTransformationMatrix(
  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 <- monsterMonsterNI(yeast$motif,yeast$exp.cc[1:1000,1:20])
cc.net.2 <- monsterMonsterNI(yeast$motif,yeast$exp.cc[1:1000,31:50])
monsterTransformationMatrix(cc.net.1, cc.net.2)

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