# Molecular Signature identification using Biclustering

## Documentation for package ‘mosbi’ version 1.8.0

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

## Help Pages

algohistogram | Get list the list of algorithms from a list of bicluster objects.
apply_threshold | Apply a threshold to a bicluster similarity adjacency matrix or a co-occurrence adjacency matrix.
apply_threshold-method | Apply a threshold to a bicluster similarity adjacency matrix.
apply_threshold-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 | A S4 class to store biclusters.
bicluster-class | A S4 class to store biclusters.
bicluster_heatmap | Plot a heatmap of a bicluster
bicluster_heatmap-method | Plot a heatmap of a bicluster
bicluster_net | A S4 class to store bicluster networks.
bicluster_net-class | A S4 class to store bicluster networks.
bicluster_network | Generate a bicluster network
bicluster_net_to_igraph | Convert Bicluster network to an igraph graph object
bicluster_net_to_igraph-method | Convert Bicluster network to an igraph graph object
bicluster_to_matrix | Convert a bicluster object to an acutal submatrix of the original matrix.
bicluster_to_matrix-method | Convert a bicluster object to an acutal submatrix of the original matrix.
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 | A S4 class to store co-occurence networks.
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-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-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 biclusters, that do not fulfill the minimum number of rows and columns. Utilizes the function 'validate_bicluster'.
filter_matrix | Filter a matrix
filter_subsets | Remove all biclusters from a list, that are identical or perfect subsets from each other. Additionally all invalid biclusters are removed (See 'validate_bicluster').
full_graph | Generate a similarity network for a list of biclusters
getAkmbiclustClusters | Extract a list of bicluster objects from an akmbiclust biclustering object.
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 biclustering object.
getBiclustClusters | Extract a list of bicluster objects from a biclust object.
getBiclustpyClusters | Extract a list of bicluster objects from an biclustpy output file.
getFabiaClusters | Extract a list of bicluster objects from an fabia biclustering object.
getIsaClusters | Extract a list of bicluster objects from an isa2 biclustering object.
getQUBIC2biclusters | Extract QUBIC2 biclusters
get_adjacency | Get Adjacency matrix
get_adjacency-method | Get Adjacency matrix
get_algorithms | Get Algorithms
get_biclusters | Extract biclusters from different algorithms/packages
get_bic_net_algorithms | Get bicluster network algorithms
get_bic_net_algorithms-method | Get bicluster network algorithms
get_louvain_communities | Get louvain communities from a bicluster network
get_louvain_communities-method | Get louvain communities from a bicluster network
get_louvain_communities-method | Get louvain communities from a co-occurrence network
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 identical to another bicluster.
mouse_data | Mouse brain lipidomics data
network_edge_strength | Count edges in an adjacency matrix using different cut-off thresholds.
network_edge_strength_float | Count edges in an adjacency matrix using different cut-off thresholds.
NoBFBiclusters | Get the number of biclusters, generated by the Bi-Force algorithm.
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-method | Plot a bicluster network
plot-method | Plot a co-occurrence network
plot_algo_network | Plot a bicluster network colored by algorithms.
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 one of two dimensional samples
p_overlap_higher | Probability for an overlap higher or equal to the observed one of two samples
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-method | Create a subset of biclusters based on a bicluster network
set_bicluster_names | Add row-/colnames to a bicluster object.
set_bicluster_names-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 at least one row and one column.
write_graphml | Save adjacency matrix as GraphML file
write_matrix | Write an R matrix to a file (In a Bi-Force or QUBIC2 readable format).
zero_subsetting | Make a vector of R indices compatible with c++ by substracting every element by one.