abcd_anxiety            Mock ABCD anxiety data
abcd_colour             Mock ABCD "colour" data
abcd_cort_sa            Mock ABCD cortical surface area data
abcd_cort_t             Mock ABCD cortical thickness data
abcd_depress            Mock ABCD depression data
abcd_h_income           Mock ABCD income data
abcd_income             Mock ABCD income data
abcd_pubertal           Mock ABCD pubertal status data
abcd_subc_v             Mock ABCD subcortical volumes data
add_settings_df_rows    Add rows to a settings_df
age_df                  Mock age data
alluvial_cluster_plot   Alluvial plot of patients across cluster counts
                        and important features
anxiety                 Mock ABCD anxiety data
as.data.frame.data_list
                        Coerce a 'data_list' class object into a
                        'data.frame' class object
as.data.frame.ext_solutions_df
                        Coerce a 'ext_solutions_df' class object into a
                        'data.frame' class object
as.data.frame.settings_df
                        Coerce a 'settings_df' class object into a
                        'data.frame' class object
as.data.frame.snf_config
                        Coerce a 'settings_df' class object into a
                        'data.frame' class object
as.data.frame.solutions_df
                        Coerce a 'solutions_df' class object into a
                        'data.frame' class object
as.data.frame.t_ext_solutions_df
                        Coerce a 't_ext_solutions_df' class object into
                        a 'data.frame' class object
as.data.frame.t_solutions_df
                        Coerce a 't_solutions_df' class object into a
                        'data.frame' class object
as.data.frame.weights_matrix
                        Coerce a 'weights_matrix' class object into a
                        'data.frame' class object
as.list.clust_fns_list
                        Coerce a 'clust_fns_list' class object into a
                        'list' class object
as.list.data_list       Coerce a 'data_list' class object into a 'list'
                        class object
as.list.dist_fns_list   Coerce a 'dist_fns_list' class object into a
                        'list' class object
as.list.sim_mats_list   Coerce a 'sim_mats_list' class object into a
                        'list' class object
as.list.snf_config      Coerce a 'snf_config' class object into a
                        'list' class object
as.matrix.ari_matrix    Coerce a 'ari_matrix' class object into a
                        'matrix' class object
as.matrix.weights_matrix
                        Coerce a 'weights_matrix' class object into a
                        'matrix' class object
as_ari_matrix           Convert an object to an ARI matrix
as_data_list            Convert an object to a data list
as_settings_df          Convert an object to a settings data frame
as_sim_mats_list        Convert an object to a similarity matrix list
as_snf_config           Convert an object to a snf config
as_weights_matrix       Convert an object to a weights matrix
assemble_data           Collapse a data frame and/or a data list into a
                        single data frame
assoc_pval_heatmap      Heatmap of pairwise associations between
                        features
auto_plot               Automatically plot features across clusters
bar_plot                Bar plot separating a feature by cluster
batch_snf               Run variations of SNF
batch_snf_subsamples    Run SNF clustering pipeline on a list of
                        subsampled data lists
cache_a_complete_example_ext_sol_df
                        Cached example extended solutions data frame
cache_a_complete_example_lp_ext_sol_df
                        Cached example extended solutions data frame
cache_a_complete_example_sol_df
                        Cached example solutions data frame
calc_aris               Construct an ARI matrix storing inter-solution
                        similarities
calc_assoc_pval_matrix
                        Calculate p-values for all pairwise
                        associations of features in a data list
calc_nmis               Calculate feature NMIs for a data list and a
                        solutions data frame
calculate_coclustering
                        Calculate co-clustering data
cancer_diagnosis_df     Mock diagnosis data
cell_significance_fn    Place significance stars on ComplexHeatmap
                        cells
check_dataless_annotations
                        Helper function to stop annotation building
                        when no data was provided
check_hm_dependencies   Check for ComplexHeatmap and circlize
                        dependencies
check_similarity_matrices
                        Check validity of similarity matrices
clust_fns               Built-in clustering algorithms
clust_fns_list          Build a clustering algorithms list
cocluster_density       Density plot of co-clustering stability across
                        subsampled data
cocluster_heatmap       Heatmap of observation co-clustering across
                        resampled data
colour_scale            Return a colour ramp for a given vector
cort_sa                 Mock ABCD cortical surface area data
cort_t                  Mock ABCD cortical thickness data
data_list               Build a 'data_list' class object
depress                 Mock ABCD depression data
diagnosis_df            Mock diagnosis data
dist_fns                Built-in distance functions
dist_fns_list           Build a distance metrics list
dlapply                 Apply-like function for data list objects
dplyr_row_slice.ext_solutions_df
                        Function to extend dplyr to extended solutions
                        data frame objects
dplyr_row_slice.solutions_df
                        Function to extend dplyr to solutions data
                        frame objects
esm_manhattan_plot      Manhattan plot of feature-cluster association
                        p-values
estimate_nclust_given_graph
                        Estimate number of clusters for a similarity
                        matrix
expression_df           Modification of SNFtool mock data frame "Data1"
extend_solutions        Extend a solutions data frame to include
                        outcome evaluations
fav_colour              Mock ABCD "colour" data
gender_df               Mock gender data
get_complete_uids       Pull complete-data UIDs from a list of data
                        frames
get_heatmap_order       Return the row or column ordering present in a
                        heatmap
get_matrix_order        Return the hierarchical clustering order of a
                        matrix
get_pvals               Get p-values from an extended solutions data
                        frame
get_representative_solutions
                        Extract representative solutions from a matrix
                        of ARIs
income                  Mock ABCD income data
is_data_list            Test if the object is a data list
jitter_plot             Jitter plot separating a feature by cluster
label_meta_clusters     Assign meta cluster labels to rows of a
                        solutions data frame or extended solutions data
                        frame
label_propagate         Label propagate cluster solutions to
                        non-clustered observations
linear_adjust           Linearly correct data list by features with
                        unwanted signal
mc_manhattan_plot       Manhattan plot of feature-meta cluster
                        association p-values
merge.clust_fns_list    Merge 'clust_fns_list' objects
merge.data_list         Merge observations between two compatible data
                        lists
merge.dist_fns_list     Merge 'dist_fns_list' objects
merge.ext_solutions_df
                        Merge 'ext_solutions_df' objects
merge.settings_df       Merge 'settings_df' objects
merge.sim_mats_list     Merge 'sim_mats_list' objects
merge.snf_config        Merge method for SNF config objects
merge.solutions_df      Merge 'solutions_df' objects
merge.t_ext_solutions_df
                        Merge 't_ext_solutions_df' objects
merge.t_solutions_df    Merge 't_solutions_df' objects
merge.weights_matrix    Merge 'weights_matrix' objects
merge_df_list           Merge list of data frames into a single data
                        frame
methylation_df          Modification of SNFtool mock data frame "Data2"
mock_ari_matrix         Mock example of an 'ari_matrix' metasnf object
mock_clust_fns_list     Mock example of a 'clust_fns_list' metasnf
                        object
mock_data_list          Mock example of a 'data_list' metasnf object
mock_dist_fns_list      Mock example of a 'dist_fns_list' metasnf
                        object
mock_ext_solutions_df   Mock example of a 'ext_solutions_df' metasnf
                        object
mock_mc_solutions_df    Mock example of a 'mc_solutions_df' metasnf
                        object
mock_rep_solutions_df   Mock example of a 'rep_solutions_df' metasnf
                        object
mock_settings_df        Mock example of a 'settings_df' metasnf object
mock_snf_config         Mock example of a 'snf_config' metasnf object
mock_solutions_df       Mock example of a 'solutions_df' metasnf object
mock_t_solutions_df     Mock example of a 't_solutions_df' metasnf
                        object
mock_weights_matrix     Mock example of a 'weights_matrix' metasnf
                        object
new_solutions_df        Constructor for 'solutions_df' class object
plot.ari_matrix         Heatmap of pairwise adjusted rand indices
                        between solutions
plot.data_list          Plot of feature values in a data list
plot.ext_solutions_df   Plot of cluster assignments in an extended
                        solutions data frame
plot.snf_config         Heatmap for visualizing an SNF config
plot.solutions_df       Plot of cluster assignments in a solutions data
                        frame
print.ari_matrix        Print method for class 'ari_matrix'
print.clust_fns_list    Print method for class 'clust_fns_list'
print.data_list         Print method for class 'data_list'
print.dist_fns_list     Print method for class 'dist_fns_list'
print.ext_solutions_df
                        Print method for class 'ext_solutions_df'
print.settings_df       Print method for class 'settings_df'
print.sim_mats_list     Print method for class 'sim_mats_list'
print.snf_config        Print method for class 'snf_config'
print.solutions_df      Print method for class 'solutions_df'
print.t_ext_solutions_df
                        Print method for class 't_ext_solutions_df'
print.t_solutions_df    Print method for class 't_solutions_df'
print.weights_matrix    Print method for class 'weights_matrix'
pubertal                Mock ABCD pubertal status data
pval_heatmap            Heatmap of p-values
quality_measures        Quality metrics
rbind.ext_solutions_df
                        Row-binding of solutions data frame class
                        objects
rbind.solutions_df      Row-binding of solutions data frame class
                        objects
rbind.t_solutions_df    Row-binding of t_solutions_df class objects
rbind.weights_matrix    Row-bind weights matrices
rename_dl               Rename features in a data list
resample                Helper resampling function found in ?sample
save_heatmap            Save a heatmap object to a file
settings_df             Build a settings data frame
shiny_annotator         Launch a shiny app to identify meta cluster
                        boundaries
sim_mats_list           Create or extract a 'sim_mats_list' class
                        object
similarity_matrix_heatmap
                        Plot heatmap of similarity matrix
siw_euclidean_distance
                        Squared (including weights) Euclidean distance
snf_config              Define configuration for generating a set of
                        SNF-based cluster solutions
split_parser            Helper function to determine which row and
                        columns to split on
str.ari_matrix          Structure of a 'ari_matrix' object
str.clust_fns_list      Structure of a 'clust_fns_list' object
str.data_list           Structure of a 'data_list' object
str.dist_fns_list       Structure of a 'dist_fns_list' object
str.ext_solutions_df    Structure of a 'ext_solutions_df' object
str.settings_df         Structure of a 'settings_df' object
str.sim_mats_list       Structure of a 'sim_mats_list' object
str.snf_config          Structure of a 'snf_config' object
str.solutions_df        Structure of a 'solutions_df' object
str.t_ext_solutions_df
                        Structure of a 't_ext_solutions_df' object
str.t_solutions_df      Structure of a 't_solutions_df' object
str.weights_matrix      Structure of a 'weights_matrix' object
subc_v                  Mock ABCD subcortical volumes data
subsample_dl            Create subsamples of a data list
subsample_pairwise_aris
                        Calculate pairwise adjusted Rand indices across
                        subsamples of data
summary.ari_matrix      Summary method for class 'ari_matrix'
summary.clust_fns_list
                        Summary method for class 'clust_fns_list'
summary.data_list       Summary method for class 'data_list'
summary.dist_fns_list   Summary method for class 'dist_fns_list'
summary.ext_solutions_df
                        Summary method for class 'ext_solutions_df'
summary.settings_df     Summary method for class 'settings_df'
summary.sim_mats_list   Summary method for class 'sim_mats_list'
summary.snf_config      Summary method for class 'snf_config'
summary.solutions_df    Summary method for class 'solutions_df'
summary.t_ext_solutions_df
                        Summary method for class 't_ext_solutions_df'
summary.t_solutions_df
                        Summary method for class 't_solutions_df'
summary.weights_matrix
                        Summary method for class 'weights_matrix'
train_test_assign       Training and testing split
uids                    Pull UIDs from an object
validate_solutions_df   Validator for 'solutions_df' class object
var_manhattan_plot      Manhattan plot of feature-feature association
                        p-values
weights_matrix          Generate a matrix to store feature weights
