Molecular Signature identification using Biclustering


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Documentation for package ‘mosbi’ version 1.4.0

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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.