R/driveR.R

In driveR: Prioritizing Cancer Driver Genes Using Genomics Data

#' driveR: An R Package for Prioritizing Cancer Driver Genes Using Genomics Data
#'
#' Cancer genomes contain large numbers of somatic alterations but few genes
#' drive tumor development. Identifying cancer driver genes is critical
#' for precision oncology. Most of current approaches either identify driver
#' genes based on mutational recurrence or using estimated scores predicting
#' the functional consequences of mutations.
#'
#' driveR is a tool for personalized or batch analysis of genomic data for
#' driver gene prioritization by combining genomic information and prior
#' biological knowledge. As features, driveR uses coding impact metaprediction
#' scores, non-coding impact scores, somatic copy number alteration scores,
#' hotspot gene/double-hit gene condition, 'phenolyzer' gene scores and
#' memberships to cancer-related KEGG pathways. It uses these features to
#' estimate cancer-type-specific probabilities for each gene of being a cancer
#' driver using the related task of a multi-task learning classification model.
#'
#'
#' @seealso \code{\link{predict_coding_impact}} for metaprediction of impact of
#' coding variants.
#' \code{\link{create_features_df}} for creating the features table to
#' be used to prioritize cancer driver genes.
#' See \code{\link{prioritize_driver_genes}} for prioritizing cancer driver genes
#'
#' @name driveR
"_PACKAGE"