Package: DrDimont 0.1.4

DrDimont: Drug Response Prediction from Differential Multi-Omics Networks

While it has been well established that drugs affect and help patients differently, personalized drug response predictions remain challenging. Solutions based on single omics measurements have been proposed, and networks provide means to incorporate molecular interactions into reasoning. However, how to integrate the wealth of information contained in multiple omics layers still poses a complex problem. We present a novel network analysis pipeline, DrDimont, Drug response prediction from Differential analysis of multi-omics networks. It allows for comparative conclusions between two conditions and translates them into differential drug response predictions. DrDimont focuses on molecular interactions. It establishes condition-specific networks from correlation within an omics layer that are then reduced and combined into heterogeneous, multi-omics molecular networks. A novel semi-local, path-based integration step ensures integrative conclusions. Differential predictions are derived from comparing the condition-specific integrated networks. DrDimont's predictions are explainable, i.e., molecular differences that are the source of high differential drug scores can be retrieved. Our proposed pipeline leverages multi-omics data for differential predictions, e.g. on drug response, and includes prior information on interactions. The case study presented in the vignette uses data published by Krug (2020) <doi:10.1016/j.cell.2020.10.036>. The package license applies only to the software and explicitly not to the included data.

Authors:Katharina Baum [cre], Pauline Hiort [aut], Julian Hugo [aut], Spoorthi Kashyap [aut], Nataniel Müller [aut], Justus Zeinert [aut]

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42 exports 0.00 score 126 dependencies 2 scripts 330 downloads

Last updated 2 years agofrom:f53860998a. Checks:OK: 3 NOTE: 4. Indexed: yes.

Exports:%>%calculate_interaction_scorecheck_connectioncheck_drug_targetcheck_drug_targets_in_layerscheck_inputcheck_layercheck_sensible_connectionschunkchunk_2gethercombine_graphscompute_correlation_matricescompute_drug_response_scorescorPvalueStudentParallelcreate_unique_layer_node_idsdetermine_drug_targetsdrdimont_settingsfind_targetsgenerate_combined_graphsgenerate_differential_score_graphgenerate_individual_graphsgenerate_interaction_score_graphsgenerate_reduced_graphget_layerget_layer_settinggraph_metricsinstall_python_dependenciesinter_layer_edgelist_by_idinter_layer_edgelist_by_tableload_interaction_score_outputmake_connectionmake_drug_targetmake_layernetwork_reduction_by_p_valuenetwork_reduction_by_pickHardThresholdreturn_errorsrun_pipelinesample_sizeset_clustershutdown_clustertarget_edge_listwrite_interaction_score_input

Dependencies:AnnotationDbiaskpassbackportsbase64encBiobaseBiocGenericsBiostringsbitbit64blobbslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdigestdoParalleldplyrdynamicTreeCutevaluatefansifarverfastclusterfastmapfontawesomeforeachforeignFormulafsgenericsGenomeInfoDbGenomeInfoDbDataggplot2glueGO.dbgridExtragtableherehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngpreprocessCoreprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppGSLRcppParallelRcppTOMLRcppZigguratreadrreticulateRfastrlangrmarkdownrpartrprojrootRSQLiterstudioapiS4VectorssassscalesstringistringrsurvivalsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisviridisLitevroomWGCNAwithrxfunXVectoryamlzlibbioc