annotate_paths          Annotates functions to pathways
brca                    BRCA gene expression dataset as
                        SummarizedExperiment
brca_data               BRCA gene expression dataset
brca_design             BRCA experimental design
comp                    Wilcoxon comparison of pathways object
create_report           Create visualization HTML
do_pca                  Performs a Principal Components Analysis
do_wilcoxon             Apply Wilcoxon test
exp_data                Normalized BRCA gene expression dataset
get_go_names            Tranlates GO IDs to GO names
get_highest_sig_ancestor
                        Get highest common GO ancestor of GO
                        annotations
get_node_names          Tranlates node IDs to node names
get_nodes_data          Gets the object of node activation values
get_path_names          Tranlates path IDs to path names
get_paths_data          Gets the object of subpathway activation values
get_pathway_functions   Returns functions related to a pathway
get_pathways_annotations
                        Get Pathways functional annotations
get_pathways_list       Lists the IDs of the pathways in a pathways
                        object
get_pathways_summary    Compute pathway summary
go_vals                 Gene Ontology matrix of the BRCA gene
                        expression dataset
heatmap_plot            Plots subpathways heatmap
hhead                   Head function for SummarizedExperiment,
                        data.frames and matrix objects
hipathia                Computes the level of activation of the
                        subpathways for each of the samples
igraphs_upgrade         Upgrade igraphs to current version
is_accepted_species     Checks whether a species is accepted
load_annofuns           Loads annotations object
load_annots             Loads functional annotations to genes
load_entrez_hgnc        Loads table of translation from HGNC to Entrez
load_gobp_frame         Loads GO graph information
load_gobp_net           Loads GO graph
load_mgi                Loads object with graph information
load_pathways           Loads the pathways object.
load_pseudo_mgi         Loads object with pseudo graph information
load_xref               Loads table of references
mgi_from_sif            Create a Pathways object from SIF files
multiple_pca_plot       Plots multiple components of a PCA
node_color              Get colors of the nodes from a comparison file
node_color_per_de       Colors of the nodes by its differential
                        expression
normalize_data          Normalize expression data from a
                        SummarizedExperiment or matrix to be used in
                        'hipathia'
normalize_paths         Normalize the pathway matrix by rows
path_vals               Pathways matrix of the BRCA gene expression
                        dataset
paths_to_go_ancestor    Create path results table with highest
                        significant GO ancestors
pathway_comparison_plot
                        Plots pathway with colored significant paths
pca_plot                Plots two components of a PCA
quantify_terms          Computes the level of activation of the
                        functions related to the previously computed
                        subpathways
results                 Results object
save_results            Save results to folder
top_pathways            Computes pathway significance
translate_data          Translation of the rownames IDs of a
                        SummarizedExperiment to Entrez IDs.
translate_matrix        Translation of the rownames IDs of a matrix to
                        Entrez IDs.
visualize_report        Visualize a HiPathia report
