Selection, Reverse-Engineering and Prediction in Cascade Networks


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Documentation for package ‘Cascade’ version 2.0

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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.