Selection, Reverse-Engineering and Prediction in Cascade Networks

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Documentation for package ‘Cascade’ version 2.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

Cascade-package	The Cascade Package: Selection, Reverse-Engineering and Prediction in Cascade Networks
analyze_network	Analysing the network
analyze_network-method	Analysing the network
analyze_network-methods	Analysing the network
as.micro_array	Coerce a matrix into a micro_array object.
Cascade	The Cascade Package: Selection, Reverse-Engineering and Prediction in Cascade Networks
compare	Some basic criteria of comparison between actual and inferred network.
compare-method	Some basic criteria of comparison between actual and inferred network.
compare-methods	Some basic criteria of comparison between actual and inferred network.
cutoff	Choose the best cutoff
cutoff-method	Choose the best cutoff
cutoff-methods	Choose the best cutoff
dim	Dimension of the data
dim-method	Dimension of the data
dim-methods	Dimension of the data
evolution	See the evolution of the network with change of cutoff
evolution-method	See the evolution of the network with change of cutoff
evolution-methods	See the evolution of the network with change of cutoff
geneNeighborhood	Find the neighborhood of a set of nodes.
geneNeighborhood-method	Find the neighborhood of a set of nodes.
geneNeighborhood-methods	Find the neighborhood of a set of nodes.
genePeakSelection	Methods for selecting genes
genePeakSelection-method	Methods for selecting genes
genePeakSelection-methods	Methods for selecting genes
geneSelection	Methods for selecting genes
geneSelection-method	Methods for selecting genes
geneSelection-methods	Methods for selecting genes
gene_expr_simulation	Simulates microarray data based on a given network.
gene_expr_simulation-method	Simulates microarray data based on a given network.
gene_expr_simulation-methods	Simulates microarray data based on a given network.
head-method	Overview of a micro_array object
head-methods	Overview of a micro_array object
inference	Reverse-engineer the network
inference-method	Reverse-engineer the network
inference-methods	Reverse-engineer the network
M	Simulated M data for examples.
methods	Overview of a micro_array object
micropredict-class	Class '"micropredict"'
micro_array-class	Class '"micro_array"'
Net	Simulated network data for examples.
network	A network object data.
network-class	Class '"network"'
network_random	Generates a network.
Net_inf	Reverse-engineered network of the simulated data.
plot-method	Plot
plot-methods	Plot
position	Returns the position of edges in the network
position-method	Returns the position of edges in the network
position-methods	Returns the position of edges in the network
predict	Prediction of the gene expressions after a knock-out experience 'predict'
predict-method	Prediction of the gene expressions after a knock-out experience 'predict'
predict-methods	Prediction of the gene expressions after a knock-out experience 'predict'
print-method	Methods for Function 'print'
print-methods	Methods for Function 'print'
Selection	Selection of genes.
summary-method	Methods for Function 'summary'
summary-methods	Methods for Function 'summary'
unionMicro	Makes the union between two micro_array objects.
unionMicro-method	Makes the union between two micro_array objects.
unionMicro-methods	Makes the union between two micro_array objects.