R/Bric.R

In carter-allen/IRISFGM: Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

#' @name qubic
#' @title qubic
#' @description  QUBIC Performs a QUalitative BIClustering.
#'
#' @param i input 
#' @param N index
#' @param R index
#' @param Fa index
#' @param d index
#' @param D index
#' @param C index
#' @param n index
#' @param q index
#' @param f index
#' @param k index
#' @param c index
#' @param o index
#'
#'
#' @importFrom Rcpp evalCpp


qubic <- function(i = NULL, 
                  N = FALSE, 
                  R = FALSE, 
                  Fa = FALSE, 
                  d = FALSE, 
                  D = FALSE, 
                  C = FALSE, 
                  n = FALSE, 
                  q = 0.05, 
                  f = 0.85, 
                  k = 13, 
                  c = 0.9, 
                  o = 100) {
    vec <- c("./qubic", "-i", i)
    if (N) 
        vec <- c(vec, "-N")
    if (R) 
        vec <- c(vec, "-R")
    if (Fa) 
        vec <- c(vec, "-F")  # only do discretization
    if (d) 
        vec <- c(vec, "-d")  # input binrary e.g. chars
    if (D) 
        vec <- c(vec, "-D")
    if (n) 
        vec <- c(vec, "-n")
    if (C) 
        vec <- c(vec, "-C")
    vec <- c(vec, "-q", as.character(q))
    vec <- c(vec, "-f", as.character(f))
    vec <- c(vec, "-k", as.character(k))
    vec <- c(vec, "-c", as.character(c))
    vec <- c(vec, "-o", as.character(o))
    
    unloadNamespace("IRISFGM")
    ret <- .main(vec)
    if (ret == 42) 
        return(qubic(paste0(i, ".chars"), d = TRUE))
    # return (ret)
}


.onUnload <- function(libpath) {
    library.dynam.unload("IRISFGM", libpath)
}