Man pages for Patterns
Deciphering Biological Networks with Patterned Heterogeneous Measurements
| analyze_network-omics_network-method | 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... |
| 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... |
| 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 |
| gene_expr_simulation-omics_network-method | Simulates omicsarray data based on a given network. |
| geneNeighborhood-omics_network-method | Find the neighborhood of a set of nodes. |
| geneSelection | Methods for selecting genes |
| head-omics_array-method | Overview of a omics_array object |
| IndicFinit | Create initial F matrices using specific intergroup actions... |
| IndicFshape | Create F matrices using specific intergroup actions for... |
| inference | Reverse-engineer the network |
| infos | Details on some probesets of the affy_hg_u133_plus_2... |
| M | Simulated microarray. |
| Net | Simulated network for examples. |
| Net_inf_PL | Reverse-engineered network of the M and Net simulated data. |
| 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"' |
| Patterns-package | Patterns: Deciphering Biological Networks with Patterned... |
| plotF | Plot functions for the F matrices. |
| plot-methods | Plot |
| 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... |
| replaceUp | Replace matrix values triangular upper part and by band for... |
| Selection | Selection of genes. |
| show-methods | 'Show' methods |
| summary-methods | 'Summary' methods |
| unionOmics-methods | Makes the union between two omics_array objects. |
| unsupervised_clustering_auto_m_c-omics_array-method | Cluster a omics_array object: determine optimal fuzzification... |
| unsupervised_clustering-omics_array-numeric-numeric-method | Cluster a omics_array object: performs the clustering. |
