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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> )
Analysing the network
as.omics_array()
Coerce a matrix into a omics_array object.
clustExploration(<omics_array> )
A function to explore a dataset and cluster its rows.
clustInference(<omics_array> ,<numeric> )
A function to explore a dataset and cluster its rows.
compare(<omics_network> ,<omics_network> ,<numeric> )
Some basic criteria of comparison between actual and inferred network.
cutoff(<omics_network> )
Choose the best cutoff
dim(<omics_array> )
Dimension of the data
doc
Human transcription factors from HumanTFDB
evolution(<omics_network> )
See the evolution of the network with change of cutoff
geneNeighborhood(<omics_network> )
Find the neighborhood of a set of nodes.
geneSelection(<omics_array> ,<omics_array> ,<numeric> ) geneSelection(<list> ,<list> ,<numeric> ) genePeakSelection(<omics_array> ,<numeric> )
Methods for selecting genes
gene_expr_simulation(<omics_network> )
Simulates omicsarray data based on a given network.
head(<omics_array> )
Overview of a omics_array object
inference(<omics_array> )
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(<omics_array> ,<ANY> ) plot(<omics_network> ,<ANY> ) plot(<omics_predict> ,<ANY> )
Plot
plotF()
Plot functions for the F matrices.
position(<omics_network> )
Returns the position of edges in the network
predict(<omics_array> )
Methods for Function predict
probeMerge(<omics_array> )
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(<omics_array> ) show(<omics_network> )
Show methods
summary(<omics_array> )
Summary methods
unionOmics(<omics_array> ,<omics_array> )
Makes the union between two omics_array objects.
unsupervised_clustering(<omics_array> ,<numeric> ,<numeric> )
Cluster a omics_array object: performs the clustering.
unsupervised_clustering_auto_m_c(<omics_array> )
Cluster a omics_array object: determine optimal fuzzification parameter and number of clusters.
