Deciphering Biological Networks with Patterned Heterogeneous Measurements

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Documentation for package ‘Patterns’ version 1.6

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

Help Pages

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
doc	Human transcription factors from HumanTFDB
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"'
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.