# HiPathia: High-throughput Pathway Analysis

## Documentation for package ‘hipathia’ version 3.12.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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
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).
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_nodes_data | Gets the object of node activation values
get_node_names | Tranlates node IDs to node names
get_paths_data | Gets the object of subpathway activation values
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
get_pathway_functions | Returns functions related to a pathway
get_path_names | Tranlates path IDs to path names
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
paths_to_go_ancestor | Create path results table with highest significant GO ancestors
pathways | Pathways object including pathways has03320 and hsa04012.
pathway_comparison_plot | Plots pathway with colored significant paths
path_vals | Pathways matrix of the BRCA gene expression dataset
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