Man pages for baumbachlab/keypathwayminer-R
KeyPathwayMiner R-Package
| base64EncFile | Method for base64 encoding |
| call_kpm_local | Method for running KeyPathwayMineR localy |
| call_kpm_remote | Method for running KeyPathwayMineR remotely |
| check_files | Function which checks and processes files |
| check_parameters | Function which check parameters |
| combine_mutliple_matrices | Logically combines multiple datasets |
| compute_z_scores | Computes z-score values of case samples |
| Configuration-class | A configuration of the parameters K and L |
| create_indicator_from_fcurdleTest | Creates indicator matrix from differentail |
| create_sca.Seurat | Converts Seurat object to SingleCellAssay object |
| create_sca.SingleCellExperiment | Converts SingleCellExperiment object to SingleCellAssay... |
| create_union_network | Creates a union network for the pathways of a specific... |
| dataset_list | Encodes a list of datasets |
| determine_union_groups | Determines from which pathways a node originates |
| do_diff_testing_via_MAST | Calculates differentially expressed genes from single cell... |
| export_graph | Export a graph |
| export_matrix | Saves indicator matrix as a file. |
| export_nodes | Export node ids |
| export_to_iGraph | Get an iGraph object for a specific pathway |
| fetch_results | Once the run is complete, we can obtain the results |
| filter_fcHurdleTestResults | Filters the differential expression analysis results based on... |
| get_case_exceptions | Creates java arguments for case exceptions |
| get_configuration | Get configuration object |
| get_configurations | Get all configuration names of a result |
| get_networks | Get a data frame of available networks |
| get_pathway | Get specific pathway of a configuration |
| get_pathways | Get all pathways for a specific configuration |
| get_results | Fetches result for remote run. |
| get_results_from_folder | Loads results from folder with text files |
| get_result_url | Returns result url |
| get_started | Functions which prints information on how to get started. |
| get_status | Method to check up on a submitted job. |
| graph_kpm | Helper method to encode custom network file |
| igraph_to_sif | Converts igraph object to sif file. |
| import_graph | Reads graph file and converts it to igraph object |
| is_finished | Check if asynchronous remote run is finished |
| kpm | Main method used for running KPM |
| kpm_options | Set or get options for KeyPathwayMineR |
| Pathway-class | A pathway of a specific configuration. |
| pathway_comparison_plots | Two pathway comparison plots. |
| pathway_statistics | Computes pathway statistics for all pathways in a result... |
| profile_pathway | Run gprofiler2's gost function on pathway of interesst |
| quest_progress_url | Get progress url |
| remove_configuration | Removes configuration from result object |
| reset_options | Resets kpm_options to default values |
| Result-class | Result |
| ResultRemote-class | ResultRemote |
| retrieve_biogrid | Retrieves bioGRID network in suitable form for KPM |
| save_local_results | Save results of the local run |
| save_remote_results | Save results of the remote run |
| sc_to_indicator_matrix | Calculates differentially expressed genes from single cell... |
| set_avg_exp | Set average differential expressed cases per gene |
| set_num_edges | Set number of edges given pathway object |
| set_num_nodes | Set number of nodes given pathway object |
| set_pathway | Set pathway |
| setup_kpm | Set up a JSON object in preparation of the job submission |
| sif_to_igraph | Convert sif file to iGraph object |
| submit_kpm | Method for submitting a job to KeyPathwayMinerWeb Submits can... |
| test_jvm | Checks the version of the JVM. |
| to_indicator_matrix | Convertes numerical matrix to an indicator matrix |
| to_java_arguments | Method which transform kpm_options() to java arguments. |
| visualize_result | Shiny App for KeyPathwayMineR results |
| withTryCatch | Helper method for error handling |
