wext: Weighted Exclusivity Test (WExT)

#' The Weighted-Exclusivity Test
#'
#' The wext package performs the exclusivity tests described by Leiserson et al.
#' in "A Weighted Exact Test for Mutually Exclusive Mutations in Cancer"
#' (Bioinformatics, 2016).
#'
#' The somatic mutations in the pathways that drive cancer development tend to
#' be mutually exclusive across tumors, providing a signal for distinguishing
#' driver mutations from a larger number of random passenger mutations. This
#' mutual exclusivity signal can be confounded by high and highly variable
#' mutation rates across a cohort of samples. Current statistical tests for
#' exclusivity that incorporate both per-gene and per-sample mutational
#' frequencies are computationally expensive and have limited precision.
#'
#' WExT is a weighted exact test for assessing the significance of mutual
#' exclusivity in an arbitrary number of mutational events. It conditions on the
#' number of samples with a mutation as well as per-event, per-sample mutation
#' probabilities. We provide a recursive formula to compute *P*-values for the
#' weighted test exactly as well as a highly accurate and efficient saddle-point
#' approximation of the test.
#'
#' \href{https://github.com/raphael-group/wext}{The Weighted Exclusivity Test (WExT)}
#' was developed by the \href{http://compbio.cs.brown.edu/}{Raphael research group}
#' at Brown University and originally implemented as a command line tool running
#' in Python. This is an adaptation for R with specific intention to be
#' compatible with the \href{https://www.tidyverse.org}{'tidyverse'}.
#'
#' @name wext
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## usethis namespace: start
#' @useDynLib wext, .registration = TRUE
#' @importFrom Rcpp sourceCpp
## usethis namespace: end
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