Man pages for tdrose/mosbi
Molecular Signature identification using Biclustering
| algohistogram | Get list the list of algorithms from a list of bicluster... |
| apply_threshold | Apply a threshold to a bicluster similarity adjacency matrix... |
| apply_threshold-bicluster_net-method | Apply a threshold to a bicluster similarity adjacency matrix. |
| apply_threshold-cooccurrence_net-method | Apply a threshold to a co-occurrence adjacency matrix. |
| attributeConnector | Extract the class-wise degree of an adjacency matrix. |
| attribute_graph | Generate attribute specific co-occurance networks. |
| attr_overlap | Count how often row/column elements occur in biclusters. |
| bicluster-class | A S4 class to store biclusters. |
| bicluster_heatmap | Plot a heatmap of a bicluster |
| bicluster_heatmap-bicluster-matrix-method | Plot a heatmap of a bicluster |
| bicluster_net-class | A S4 class to store bicluster networks. |
| bicluster_net_to_igraph | Convert Bicluster network to an igraph graph object |
| bicluster_net_to_igraph-bicluster_net-method | Convert Bicluster network to an igraph graph object |
| bicluster_network | Generate a bicluster network |
| bicluster_to_matrix | Convert a bicluster object to an acutal submatrix of the... |
| bicluster_to_matrix-matrix-bicluster-method | Convert a bicluster object to an acutal submatrix of the... |
| check_names | Throw an error, if a matrix has not both row- and colnames. |
| clean_bicluster_list | Clean a list of biclusters, by returning only the valid ones, |
| colhistogram | Get the columnlengths for a list of bicluster objects. |
| cooccurrence_net-class | A S4 class to store co-occurence networks. |
| cooccurrence_net_to_igraph | Convert a co-occurence network to an igraph graph object |
| cooccurrence_net_to_igraph-cooccurrence_net-method | Convert a co-occurrence to an igraph graph object |
| cpp_matrix_subsetting | Subsetting of R matrices within c++. |
| detect_elements | Detect the number of elements in a list of biclusters. |
| dim-bicluster-method | Get the dimensions of a bicluster. |
| distance_matrix | Compute distances between biclusters |
| ensemble_biclusters | Convert communities into ensemble biclusters |
| feature_louvain_overlap | Overlap of features/samples in different louvain communities |
| feature_network | Generate a co-occurence network |
| filter_biclusters | Filter biclusters based on a user defined filter function. |
| filter_bicluster_size | Filter a list of bicluster objects, by erasing all... |
| filter_matrix | Filter a matrix |
| filter_subsets | Remove all biclusters from a list, that are identical or... |
| full_graph | Generate a similarity network for a list of biclusters |
| get_adjacency | Get Adjacency matrix |
| get_adjacency-bicluster_net-method | Get Adjacency matrix |
| getAkmbiclustClusters | Extract a list of bicluster objects from an akmbiclust... |
| get_algorithms | Get Algorithms |
| getallBFClusters | Get all biclusters from a Bi-Force output file. |
| getBFCluster | Get a bicluster a Bi-Force output file |
| getBicAREbiclusters | Extract a list of bicluster objects from an BicARE... |
| getBiclustClusters | Extract a list of bicluster objects from a biclust object. |
| get_biclusters | Extract biclusters from different algorithms/packages |
| getBiclustpyClusters | Extract a list of bicluster objects from an biclustpy output... |
| get_bic_net_algorithms | Get bicluster network algorithms |
| get_bic_net_algorithms-bicluster_net-method | Get bicluster network algorithms |
| getFabiaClusters | Extract a list of bicluster objects from an fabia... |
| getIsaClusters | Extract a list of bicluster objects from an isa2 biclustering... |
| get_louvain_communities | Get louvain communities from a bicluster network |
| get_louvain_communities-bicluster_net-method | Get louvain communities from a bicluster network |
| get_louvain_communities-cooccurrence_net-method | Get louvain communities from a co-occurrence network |
| getQUBIC2biclusters | Extract QUBIC2 biclusters |
| has_names | Check, whether a matrix has row- and colnames. |
| is_subset_or_identical | Check if a bicluster is a subset (in rows AND columns) of... |
| mouse_data | Mouse brain lipidomics data |
| network_edge_strength | Count edges in an adjacency matrix using different cut-off... |
| network_edge_strength_float | Count edges in an adjacency matrix using different cut-off... |
| NoBFBiclusters | Get the number of biclusters, generated by the Bi-Force... |
| node_size | Node sizes for plotting bicluster networks. |
| occurance_matrix | Occurance matrix of data points in a list of biclusters |
| occurance_table | Occurance table of data points in a list of biclusters |
| plot_algo_network | Plot a bicluster network colored by algorithms. |
| plot-bicluster_net-missing-method | Plot a bicluster network |
| plot-cooccurrence_net-missing-method | Plot a co-occurrence network |
| plot_piechart_bicluster_network | Plot a bicluster network with piecharts as nodes. |
| p_overlap | Probability for an overlap of two samples. |
| p_overlap_2d | Probability for an overlap of two dimensional samples |
| p_overlap_2d_higher | Probability for an overlap higher or equal to the observed... |
| p_overlap_higher | Probability for an overlap higher or equal to the observed... |
| randomize_matrix | Randomize a matrix |
| replace_threshold | Replace elements of an integer matrix. |
| replace_values | Replace values in an integer adjacency matrix. |
| replace_values_float | Replace values in a adjacency matrix. |
| rowhistogram | Get the rowlengths for a list of bicluster objects. |
| run_akmbiclust | Run the akmbiclust biclustering algorithm |
| run_bimax | Run the Bimax biclustering algorithm |
| run_cc | Run the CC biclustering algorithm |
| run_fabia | Run the fabia biclustering algorithm |
| run_isa | Run the isa biclustering algorithm |
| run_plaid | Run the Plaid biclustering algorithm |
| run_qubic | Run the QUBIC biclustering algorithm |
| run_quest | Run the Quest biclustering algorithm |
| run_spectral | Run the spectral biclustering algorithm |
| run_unibic | Run the UniBic biclustering algorithm |
| run_xmotifs | Run the Xmotifs biclustering algorithm |
| sample_biclusters | Sample a list of biclusters. |
| select_biclusters_from_bicluster_network | Create a subset of biclusters based on a bicluster network |
| select_biclusters_from_bicluster_network-bicluster_net-list-method | Create a subset of biclusters based on a bicluster network |
| set_bicluster_names | Add row-/colnames to a bicluster object. |
| set_bicluster_names-bicluster-matrix-method | Add row-/colnames to a bicluster object. |
| similarity_matrix | Compute similarities between biclusters |
| transpose_bicluster | Transpose a bicluster. Row and column slots will be changed. |
| validate_bicluster | Indicates, whether a bicluster is valid. That means it needs... |
| write_graphml | Save adjacency matrix as GraphML file |
| write_matrix | Write an R matrix to a file (In a Bi-Force or QUBIC2 readable... |
| zero_subsetting | Make a vector of R indices compatible with c++ by... |
