DAcomp                  Compares the gene expression, pathway
                        activation level and the function activation
                        level of the
DAdata                  Wilcoxon and limma comparison object for nodes,
                        pathways and functional annotations
DAoverview              Table and plot of total number of altered and
                        not altered nodes, paths and functions (Uniprot
                        keywords and/or GO terms, if present).
DAreport                Create visualization HTML
DAsummary               Lists and plots the top 'n' altered pathways,
                        taking into account the number of altered .
DAtop                   Lists and plots the top 'n' altered nodes,
                        paths and functions (Uniprot keywords and/or GO
                        terms, if present).
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
define_colors           Color palettes to be used in plots.
do_pca                  Performs a Principal Components Analysis
do_wilcoxon             Apply Wilcoxon test
exp_data                Normalized BRCA gene expression dataset
get_file                Loads a RData object and downloads it from
                        Zenodo if necessary
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
hidata                  Results object
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
pathways                Pathways object including pathways has03320 and
                        hsa04012.
pca_plot                Plots two components of a PCA
plotVG                  Plots a pathway with or without the comparison
                        information, using the visNetwork library.
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
