HiPathia: High-throughput Pathway Analysis


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Documentation for package ‘hipathia’ version 2.4.0

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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_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
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
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
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