# Deciphering Biological Networks with Patterned Heterogeneous Measurements

## Documentation for package ‘Patterns’ version 1.4

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

## Help Pages

Patterns-package | The Patterns Package
analyze_network | Analysing the network
analyze_network-method | Analysing the network
analyze_network-methods | Analysing the network
as.omics_array | Coerce a matrix into a omics_array object.
CascadeFinit | Create initial F matrices for cascade networks inference.
CascadeFshape | Create F matrices shaped for cascade networks inference.
CLL | Expression data from healthy and malignant (chronic lymphocytic leukemia, CLL) human B-lymphocytes after B-cell receptor stimulation (GSE 39411 dataset)
clustExploration | A function to explore a dataset and cluster its rows.
clustExploration-method | A function to explore a dataset and cluster its rows.
clustExploration-methods | A function to explore a dataset and cluster its rows.
clustInference | A function to explore a dataset and cluster its rows.
clustInference-method | A function to explore a dataset and cluster its rows.
clustInference-methods | A function to explore a dataset and cluster its rows.
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 omicsarray data based on a given network.
gene_expr_simulation-method | Simulates omicsarray data based on a given network.
gene_expr_simulation-methods | Simulates omicsarray data based on a given network.
head-method | Overview of a omics_array object
head-methods | Overview of a omics_array object
IndicFinit | Create initial F matrices using specific intergroup actions for network inference.
IndicFshape | Create F matrices using specific intergroup actions for network inference.
inference | Reverse-engineer the network
inference-method | Reverse-engineer the network
inference-methods | Reverse-engineer the network
infos | Details on some probesets of the affy_hg_u133_plus_2 platform.
M | Simulated microarray.
methods | Overview of a omics_array object
Net | Simulated network for examples.
network | A example of an inferred network (4 groups case).
network2gp | A example of an inferred cascade network (2 groups case).
networkCascade | A example of an inferred cascade network (4 groups case).
network_random | Generates a network.
Net_inf_PL | Reverse-engineered network of the M and Net simulated data.
omics_array-class | Class '"omics_array"'
omics_network-class | Class '"omics_network"'
omics_predict-class | Class '"omics_predict"'
Patterns | The Patterns Package
plot-method | Plot
plot-methods | Plot
plotF | Plot functions for the F matrices.
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 | Methods for Function 'predict'
predict-method | Methods for Function 'predict'
predict-methods | Methods for Function 'predict'
probeMerge | Function to merge probesets
probeMerge-method | Function to merge probesets
replaceBand | Replace matrix values by band.
replaceDown | Replace matrix values triangular lower part and by band for the upper part.
replaceUp | Replace matrix values triangular upper part and by band for the lower part.
Selection | Selection of genes.
show-method | 'Show' methods
show-methods | 'Show' methods
summary-method | 'Summary' methods
summary-methods | 'Summary' methods
unionOmics | Makes the union between two omics_array objects.
unionOmics-method | Makes the union between two omics_array objects.
unionOmics-methods | Makes the union between two omics_array objects.
unsupervised_clustering | Cluster a omics_array object: performs the clustering.
unsupervised_clustering-method | Cluster a omics_array object: performs the clustering.
unsupervised_clustering_auto_m_c | Cluster a omics_array object: determine optimal fuzzification parameter and number of clusters.
unsupervised_clustering_auto_m_c-method | Cluster a omics_array object: determine optimal fuzzification parameter and number of clusters.