Man pages for cannin/tumorcomparer
Compare Patient Samples to Cell Line Models Using Molecular Data and Weighted Similarity
| ballon_plot_data_to_result_table | Transforms data frame of balloon plot into data frame with... |
| calc_weighted_corr | Calculate weighted correlation |
| categorize_cell_lines | Categorize cell lines by the level of similarity to k-nearest... |
| compute_freq_alt | Computes frequency of alteration (fraction of non-zeroes) |
| convert_to_0_to_1_using_xminusmin_by_maxminusmin | Rescale between 0-1 |
| cyj_graph_maker_from_dist_mat | Creates cytoscape.js JSON graph from distance matrix for... |
| generate_composite_mat_and_gene_weights | Run a comparison between between two cohorts (e.g. cell lines... |
| graphNELtoJSON | Convert R graphNEL object to cytoscape.js JSON. |
| keep_only_high_level_cnas | Keep only high-level CNAs (set low-level CNAs to 0) |
| make_balloon_plot_data_from_comparison_result | Make Balloon Plot Data from Run Comparison Function |
| make_balloon_plot_data_from_mtc | Make Balloon Plot from MTC Data structure |
| map_mean_similarity_to_gradient | Map mean similarity of cell lines to k nearest tumors to... |
| pair_dist | Calculate a weighted distance (between two vectors) based on... |
| plot_balloon_plot | Make Balloon Plot for Results |
| plot_joyplot | Make Joy Plots for Distributions for Similarity Distributions |
| plot_mds | Plot the results from run_comparison as a two dimension... |
| return_first_part | Return first part of ID for CCLE cell line names |
| run_comparison | Run a comparison between two cohorts (e.g. cell lines and... |
| run_comparison_config_list | Run a comparison between two cohorts (e.g. cell lines and... |
| run_shiny_app | Run Shiny App |
| tcga_pancan_pathway_genes | Genes for TCGA Pan-Cancer Pathways |
| tc_geneset_comparison | Gene Set Comparison Function for TCGA Dataset |
| tic | Starts a stopwatch timer to measure performance |
| toc | Stops a stopwatch timer to measure performance |
