# Selection, Reverse-Engineering and Prediction in Cascade Networks

## Documentation for package ‘Cascade’ version 1.8

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

## Help Pages

Cascade-package | The Cascade Package
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
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.