Man pages for martahidalgo/hipathia
HiPathia: High-throughput Pathway Analysis
| 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... |
| DAoverview | Table and plot of total number of altered and not altered... |
| DAreport | Create visualization HTML |
| DAsummary | Lists and plots the top 'n' altered pathways, taking into... |
| DAtop | Lists and plots the top 'n' altered nodes, paths and... |
| 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_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... |
| hipathia | Computes the level of activation of the subpathways for each... |
| 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... |
| normalize_paths | Normalize the pathway matrix by rows |
| paths_to_go_ancestor | Create path results table with highest significant GO... |
| path_vals | Pathways matrix of the BRCA gene expression dataset |
| pathway_comparison_plot | Plots pathway with colored significant paths |
| pca_plot | Plots two components of a PCA |
| plotVG | Plots a pathway with or without the comparison information,... |
| quantify_terms | Computes the level of activation of the functions related to... |
| 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... |
| translate_matrix | Translation of the rownames IDs of a matrix to Entrez IDs. |
| visualize_report | Visualize a HiPathia report |
