Man pages for fbertran/Patterns
Deciphering Biological Networks with Patterned Heterogeneous Measurements

analyze_network-methodsAnalysing the network
as.micro_arrayCoerce a matrix into a micro_array object.
CascadeFinitCreate initial F matrices for cascade networks inference.
CascadeFshapeCreate F matrices shaped for cascade networks inference.
CLLExpression data from healthy and malignant (chronic...
clustExploration-methodsA function to explore a dataset and cluster its rows.
clustInference-methodsA function to explore a dataset and cluster its rows.
compare-methodsSome basic criteria of comparison between actual and inferred...
cutoff-methodsChoose the best cutoff
dim-methodsDimension of the data
evolution-methodsSee the evolution of the network with change of cutoff
gene_expr_simulationSimulates microarray data based on a given network.
geneNeighborhood-methodsFind the neighborhood of a set of nodes.
genePeakSelection-methodsMethods for selecting genes
head-methodsOverview of a micro_array object
IndicFinitCreate initial F matrices using specific intergroup actions...
IndicFshapeCreate F matrices using specific intergroup actions for...
inference-methodsReverse-engineer the network
infosDetails on some probesets of the affy_hg_u133_plus_2...
MSimulated microarray.
micro_array-classClass '"micro_array"'
micropred-classClass '"micropred"'
NetSimulated network for examples.
Net_inf_PLReverse-engineered network of the M and Net simulated data.
networkA example of an inferred network (4 groups case).
network2gpA example of an inferred cascade network (2 groups case).
networkCascadeA example of an inferred cascade network (4 groups case).
network-classClass '"network"'
network_randomGenerates a network.
Patterns-packageThe Patterns Package
plotFPlot functions for the F matrices.
plot-methodsPlot
positionRetrieve network position for consistent plotting.
position-methodsReturns the position of edges in the network
predict-methodsMethods for Function 'predict'
print-methods~~ Methods for Function 'print' ~~
probeMergeFunction to merge probesets
replaceBandReplace matrix values by band.
replaceDownReplace matrix values triangular lower part and by band for...
replaceUpReplace matrix values triangular upper part and by band for...
SelectionSelection of genes.
summary-methods~~ Methods for Function 'summary' ~~
unionMicro-methodsMakes the union between two micro_array objects.
unsupervised_clusteringCluster a micro_array object: performs the clustering.
unsupervised_clustering_auto_m_cCluster a micro_array object: determine optimal fuzzification...
fbertran/Patterns documentation built on Dec. 4, 2019, 1:12 p.m.