R/RcppExports.R

In bhklab/PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

#' QUICKSTOP significance testing for partial correlation
#'
#' This function will test whether the observed partial correlation is significant
#' at a level of req_alpha, doing up to MaxIter permutations. Currently, it
#' supports only grouping by discrete categories when calculating a partial correlation.
#' Currenlty, only does two sided tests.
#'
#' @param pin_x one of the two vectors to correlate.
#' @param pin_y the other vector to calculate
#' @param pobsCor the observed (partial) correlation between these varaiables
#' @param pGroupFactor an integer vector labeling group membership, to correct
#' for in the partial correlation. NEEDS TO BE ZERO BASED!
#' @param pGroupSize an integer vector of size length(unique(pGroupFactor)), counting
#' the number of members of each group (basically table(pGroupFactor)) as integer vector
#' @param pnumGroup how many groups are there (len(pGroupSize))
#' @param pMaxIter maximum number of iterations to do, as a REAL NUMBER
#' @param pn length of x and y, as a REAL NUMBER
#' @param preq_alpha the required alpha for significance
#' @param ptolerance_par the tolerance region for quickstop. Suggested to be 1/100th of req_alpha'
#' @param plog_decision_boundary log (base e) of 1/probability of incorrectly calling significance, as
#' per quickstop paper (used to determine the log-odds)
#' @param pseed A numeric vector of length 2, used to seed the internal xoroshiro128+ 1.0
#' random number generator. Note that currently, these values get modified per call, so pass in a copy
#' if you wish to keep a seed for running same simulation twice
#'
#' @return a double vector of length 4, entry 1 is either 0, 1 (for TRUE/FALSE) or NA_REAL_ for significance determination
#' NA_REAL_ is returned when the MaxIter were reached before a decision is made. Usually, this occurs when the real p value is close to, or
#' falls within the tolerance region of (req_alpha, req_alpha+tolerance_par). Entry 2 is the current p value estimate. entry 3 is the total
#' number of iterations performed. Entry 4 is the number of time a permuted value was larger in absolute value than the observed cor.
#'
#' @useDynLib PharmacoGx _PharmacoGx_partialCorQUICKSTOP
#'
#'
partialCorQUICKSTOP <- function(pin_x, pin_y, pobsCor, pGroupFactor, pGroupSize, pnumGroup, pMaxIter, pn, preq_alpha, ptolerance_par, plog_decision_boundary, pseed) {
    .Call('_PharmacoGx_partialCorQUICKSTOP', PACKAGE = 'PharmacoGx', pin_x, pin_y, pobsCor, pGroupFactor, pGroupSize, pnumGroup, pMaxIter, pn, preq_alpha, ptolerance_par, plog_decision_boundary, pseed)
}