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. |