CLL                     Expression data from healthy and malignant
                        (chronic lymphocytic leukemia, CLL) human
                        B-lymphocytes after B-cell receptor stimulation
                        (GSE 39411 dataset)
CascadeFinit            Create initial F matrices for cascade networks
                        inference.
CascadeFshape           Create F matrices shaped for cascade networks
                        inference.
IndicFinit              Create initial F matrices using specific
                        intergroup actions for network inference.
IndicFshape             Create F matrices using specific intergroup
                        actions for network inference.
M                       Simulated microarray.
Net                     Simulated network for examples.
Net_inf_PL              Reverse-engineered network of the M and Net
                        simulated data.
Selection               Selection of genes.
analyze_network,omics_network-method
                        Analysing the network
as.omics_array          Coerce a matrix into a omics_array object.
clustExploration,omics_array-method
                        A function to explore a dataset and cluster its
                        rows.
clustInference,omics_array,numeric-method
                        A function to explore a dataset and cluster its
                        rows.
compare-methods         Some basic criteria of comparison between
                        actual and inferred network.
cutoff,omics_network-method
                        Choose the best cutoff
dim                     Dimension of the data
doc                     Human transcription factors from HumanTFDB
evolution,omics_network-method
                        See the evolution of the network with change of
                        cutoff
geneNeighborhood,omics_network-method
                        Find the neighborhood of a set of nodes.
geneSelection           Methods for selecting genes
gene_expr_simulation,omics_network-method
                        Simulates omicsarray data based on a given
                        network.
head,omics_array-method
                        Overview of a omics_array object
inference               Reverse-engineer the network
infos                   Details on some probesets of the
                        affy_hg_u133_plus_2 platform.
jetsetscores            jetsetscoresHuman transcription factors from
                        HumanTFDB
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.
omics_array-class       Class '"omics_array"'
omics_network-class     Class '"omics_network"'
omics_predict-class     Class '"omics_predict"'
plot-methods            Plot
plotF                   Plot functions for the F matrices.
position-methods        Returns the position of edges in the network
predict,omics_array-method
                        Methods for Function 'predict'
probeMerge,omics_array-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.
show-methods            'Show' methods
summary-methods         'Summary' methods
unionOmics-methods      Makes the union between two omics_array
                        objects.
unsupervised_clustering,omics_array,numeric,numeric-method
                        Cluster a omics_array object: performs the
                        clustering.
unsupervised_clustering_auto_m_c,omics_array-method
                        Cluster a omics_array object: determine optimal
                        fuzzification parameter and number of clusters.
