HiPathia: High-throughput Pathway Analysis


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Documentation for package ‘hipathia’ version 3.5.0

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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
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_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