| Guess reference table used for annovar annotation | annovar_guess_reference_table |
| Check RNAseq Dataframe | assert_rnaseq_df_is_formatted_correctly |
| Assert that class is maf_data_pool | assert_that_class_is_maf_data_pool |
| Assert that class is maf_data_pool | assert_that_class_is_maf_dataset_wrapper |
| Turn Text into A Badge | badgify |
| Map logical to colour | bool_to_colour |
| Check if class is a maf_data_pool | class_is_maf_data_pool |
| Check if class is a maf_dataset_wrapper | class_is_maf_dataset_wrapper |
| Conditional UI | conditionalUI |
| #' Install dependencies #' #' @export #' install_dependencies <- function() BiocManager::install("PoisonAlien/TCGAmutations") #BiocManager::install("maftools") | create_mac_binary |
| Download MAF | download_maf |
| external_tools_add_tool_to_dataframe | external_tools_add_tool_to_dataframe |
| Conversion Function: MAF to BBGLab Cancer Genome Interpreter Input | external_tools_convert_maf_to_bbglab |
| Conversion Function: MAF to BBGLab Cancer Genome Interpreter Input | external_tools_convert_maf_to_bbglab_return_dataframe |
| MAF + Gene -> cBioPortal mutation_mapper_input | external_tools_convert_maf_to_cbioportal_mutation_mapper_return_dataframe |
| Conversion Function: MAF to BBGLab Cancer Genome Interpreter Input | external_tools_convert_maf_to_oncodrive_return_dataframe |
| Maf to VCF | external_tools_convert_maf_to_vanilla_vcf_return_dataframe |
| external_tools_get_property_by_tool_name | external_tools_get_property_by_tool_name |
| Load tool metadata into global variable | external_tools_load_all_tools |
| Load tool metadata into environment. Returns | external_tools_load_bbglab_cgi |
| Load tool metadata into global variable | external_tools_load_bbglab_oncodrive_clustl |
| Load tool metadata into global variable | external_tools_load_bbglab_oncodrive_fml |
| Load tool metadata into global variable | external_tools_load_proteinpaint |
| Update builtin external_tools dataset | external_tools_update_builtin_dataset |
| Get Width/Height of a rendered element | get_rendered_plot_height |
| Get Width/Height of a rendered element | get_rendered_plot_width |
| Get TCGA MAFs | get_tcga_mafs |
| Tabulate Gistic Gene Files | gistic_tabulate_amp_or_del_genes_file |
| Guesses mutation filetype | guess_genomic_mutation_filetype |
| HTML_alert | html_alert |
| icon_down_arrow | icon_down_arrow |
| My function | imports |
| Is a clinical_feature_file valid for a given maf | is_valid_clinicalfeaturefile |
| Is a clinical_feature_file valid for a given maf | is_valid_clinicalfeaturefile_return_error |
| Link | link |
| Add to MAF Data Pool | maf_data_pool_add_dataset |
| Add RNAseq - maf_data_pool version | maf_data_pool_add_rnaseq |
| Get Colnames for maf_data_pool to data.frame conversion | maf_data_pool_get_all_nonfunction_property_names |
| Retrieve dataset wrapper from data pool using unique_name | maf_data_pool_get_data_wrapper_from_unique_name |
| Retrieve dataset wrapper from data pool using unique_name | maf_data_pool_get_index_from_unique_name |
| Get Unique Names from Maf Data Pool | maf_data_pool_get_unique_names |
| Load a dataset wrapper from data pool using unique_name | maf_data_pool_load_data |
| Make a name unique (within datapool) | maf_data_pool_make_name_unique |
| Load MAF objects | maf_data_pool_robust_load |
| MAF Data Pool to Dataframe | maf_data_pool_to_dataframe |
| Check availability of a name in the data pool | maf_data_pool_unique_name_is_available |
| maf_data_pool_unique_name_to_maf_nonreactive | maf_data_pool_unique_name_to_maf_nonreactive |
| maf_data_pool_unique_name_to_maf_reactive | maf_data_pool_unique_name_to_maf_reactive |
| Unload dataset wrapper from data pool using unique_name | maf_data_pool_unload_data |
| Load data into memory | maf_data_set_wrapper_load_data |
| Unload data from memory | maf_data_set_wrapper_unload_data |
| Add RNAseq slot to maf_dataset_wrapper | maf_data_wrapper_add_rnaseq |
| Get Expression Data from maf | maf_data_wrapper_get_rnaseq_data_for_samples_with_mutation_data |
| Get rnaseq data | maf_data_wrapper_get_rnaseq_df |
| Maf Dataset has RNAseq data | maf_data_wrapper_has_rnaseq_data |
| add BRCA subtype clinical feature | maftools_add_brca_subtype |
| Add clindata to MAF | maftools_add_clinical_data |
| Convert chromosomes 23 and 24 to x and y in maf object. This will convert | maftools_chrom_23_and_24_to_X_and_Y |
| maftools_clinical_data_get_levels | maftools_clinical_data_get_levels |
| Plot Clinical Data Plot a particular column of clinical DATA. | maftools_clinical_data_visually_summarise |
| Get a data.frame describing each clinical feature of a MAF | maftools_clinical_feature_description |
| maftools_cluster_samples | maftools_cluster_samples |
| Extract geneset | maftools_extract_geneset_by_altered_samples |
| Type MAF clinical data | maftools_fix_clinical_data_types |
| Get MAF data | maftools_get_all_data |
| Get Longest Transcript Refseq ID | maftools_get_transcript_refseq |
| Number of samples in a MAF | maftools_number_of_samples |
| Maftools rainfallPlot Wrapper | maftools_plot_rainfall |
| Filter dubious genes from MAF | maftools_remove_dubious_genes |
| mod_data_import_step1 Server Functions | mod_data_import_maf_path_to_maf_server |
| mod_data_import_step1 UI Function | mod_data_import_maf_path_to_maf_ui |
| data_import_step_2 Server Functions | mod_data_import_step2_server |
| external_tools Server Functions | mod_external_tools_server |
| import_clinical_featurefile Server Functions | mod_import_clinical_featurefile_server |
| import_clinical_featurefile UI Function | mod_import_clinical_featurefile_ui |
| plot_apobec_diff Server Functions | mod_plot_apobec_diff_server |
| plotforest: Wraps around maftools::forestPlot to more explicitly handle pval VS fdr option and allow both to be passed while onl using the value set by bool 'threshold_on_fdr' | mod_plot_lollipop_ui |
| somatic_interactions Server Functions | mod_plot_somatic_interactions_server |
| plot_survival Server Functions | mod_plot_survival_server |
| Title | mod_render_clinical_data_table_server |
| render_clinical_data_table UI Function | mod_render_clinical_data_table_ui |
| Title | mod_render_downloadabledataframe_server |
| Select Dataset, Return maf_dataset_wrapper | mod_select_maf_dataset_wrapper_server |
| shinyfile_import Server Functions | mod_shinyfile_import_server |
| shinyfile_import UI Function | mod_shinyfile_import_ui |
| Get Path to Clinical Feature File | mod_shinyfiles_get_clinical_featurefile_path_server |
| shinyfiles_get_clinical_featurefile_path UI Function | mod_shinyfiles_get_clinical_featurefile_path_ui |
| shinyfiles_get_maf_path Server Functions | mod_shinyfiles_get_maf_path_server |
| wrapper for running multiple mod_single_cohort_summary_tables_server modules | mod_single_cohort_summary_tables_and_plots_server |
| wrapper for running multiple mod_single_cohort_summary_tables_ui modules | mod_single_cohort_summary_tables_and_plots_ui |
| Saves Plots as SVG. | moduleDownloadPlotServer |
| Creates a shinyWidgets::downloadbttn | moduleDownloadPlotUI |
| Read MAF server function | moduleReadMafServer |
| Read MAF UI function | moduleReadMafUI |
| moduleSubsetByClinicalFeaturesServer | moduleSubsetByClinicalFeaturesServer |
| Constructor Objects of Class: *maf_data_pool* | new_maf_data_pool |
| Constructor Objects of Class: *maf_dataset_wrapper* | new_maf_dataset_wrapper |
| A function that parses numbers from strings | parse_number |
| Add PCAWG dataset to a data pool | pcawg_dataset_to_data_pool |
| Create dataset wrapper from pcawg dataset | pcawg_dataset_to_maf_dataset_wrapper |
| Add all PCAWG datasets to a data pool | pcawg_datasets_to_data_pool |
| plotforest: Wraps around maftools::forestPlot to more explicitly handle pval VS fdr option and allow both to be passed while onl using the value set by bool 'threshold_on_fdr' | plotforest |
| Read MAF from ANNOVAR OR MAF input | read_maf_flexible |
| Read RNAseq file | read_rnaseq_file |
| Run the Shiny Application | run_app |
| Programmatically create a Shiny input | shinyInput |
| Add TCGA cohort to data pool | tcga_dataset_to_data_pool |
| TCGA to maf_dataset_wrapper | tcga_dataset_to_maf_dataset_wrapper |
| Adds all TCGA cohort to data pool | tcga_datasets_to_data_pool |
| Load TCGA data | TCGAmutations_load_with_typed_metadata |
| Input is non-empty string | text_is_non_zero_string |
| Title | user_data_filepath_to_class_maf_dataset_wrapper |
| Add User Data to data pool | user_to_dataset_to_data_pool |
