driveR

driveR package

driveR

driveR: An R Package for Prioritizing Cancer Driver Genes Using Genomics Data

Main functions

Main functions of driveR

predict_coding_impact()

Create Coding Impact Meta-prediction Score Data Frame

create_features_df()

Create Data Frame of Features for Driver Gene Prioritization

prioritize_driver_genes()

Prioritize Cancer Driver Genes

Utility Functions

Utility functions for generating the features

create_noncoding_impact_score_df()

Create Non-coding Impact Score Data Frame

create_gene_level_scna_df()

Create Gene-level SCNA Data Frame

create_SCNA_score_df()

Create SCNA Score Data Frame

determine_hotspot_genes()

Determine Hotspot Containing Genes

determine_double_hit_genes()

Determine Double-Hit Genes

Built-in Data

Data within the package

metapredictor_model

Random Forest Model for Coding Impact Metaprediction

TCGA_MTL_fit

Multi-Task Learning Model for Predicting Cancer Driver Genes

MTL_submodel_descriptions

MTL Sub-model Descriptions

specific_thresholds

Tumor type specific probability thresholds

MCR_table

Table of Pan-Cancer Minimal Common Regions

KEGG_cancer_pathways

KEGG "Pathways in cancer"-related Pathways - Gene Sets

KEGG_cancer_pathways_descriptions

KEGG "Pathways in cancer"-related Pathways - Descriptions

example_scna_table

Example Somatic Copy Number Alteration Table

example_cohort_scna_table

Example Cohort-level Somatic Copy Number Alteration Table

example_features_table

Example Features Table for Driver Prioritization

example_cohort_features_table

Example Cohort-level Features Table for Driver Prioritization