Molecular Signature identification using Biclustering

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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.