Man pages for paulklemm/mygo
Create Report for mus musculus dataset of GO-term analysis using clusterProfiler
| add_is_duplicated | Check if rowname is duplicated and add binary is_duplicated... |
| attach_goterm_genecount | Add count for each GO-term and calculate overlap ratio of... |
| bind_goterm_table | Combine goterms into a single data frame |
| createHTMLReport | Make GO-Term analysis and print out Report |
| emap_plot | Create clusterProfiler EMA plot from go term |
| emap_plot_facet_category | Combine emap plots into one ggplot2 plot |
| export_go_terms_to_excel | Export list of GO terms to Excel file |
| get_go_all_ontologies | Get GO-terms for all ontologies |
| get_go_all_ontologies_2 | Get GO-terms for all ontologies. This method requires a... |
| get_go_all_ontologies_helper | Helper function getting all GO-terms based on vectors of... |
| get_gse_all_ontologies | Get GSE-terms for all ontologies |
| get_kegg | Get KEGG GSE terms |
| get_kegg_table | Get Table containing Kegg pathway information 'pathway',... |
| get_named_fc_vector | Get named fc vector. Prepare input data as required by GSE |
| overlap_percentage_plot | Plot top n GO-terms w.r.t percentage of significant genes... |
| overlap_percentage_plot_facet_category | Wrapper for mygo::overlap_percentage_plot to facet all GO... |
| overlap_scatterplot | Plot total gene count against percentage of significant genes |
| perform_enrichGO | Perform a clusterPrfiler enrichGO analysis |
| perform_gseGO | Perform a clusterProfiler gseGO analysis |
| perform_gseKEGG | Perform a clusterProfiler gseKEGG analysis |
| plot_all_ontologies | Print a couple of standard plots for provided GO ontologies |
| plot_kegg | Create KEGG pathway as PNG |
| plot_png | Plot png object (e.g. from plot_kegg_pathway) |
| plot_terms_go | Print a series of clusterProfiler plots |
| plot_terms_gse | Plot GSE terms |
| print_goterm_as_datatable | Helper function, takes clusterProfiler GO-term result and... |
| run_goterms | Run GO-Term analysis and retrieve plots This is for usage in... |
| simplify_ontologies | Simplify GO terms |
| volcano_plot | Return a volcano plot with annotated top_n values |
