R/selectFromCompareGroups.R

In IRBLleida/UdBRpackage: Miscellaneous R Functions

#' @title Select differential variables between groups by significance level
#' 
#' @description Select differential variables between groups by significance level.
#' 
#' @param x an object of class 'compareGroups'
#' @param p.threshold a significance level threshold for selecting. Default value is 0.2, meaning that all variable showing an overall p-value under 0.2 will be setected.
#' @param which.p name of p-value from x to compare with threshold of 'relevant' value. Default value is p.overall. Other options are: p.ratio (p.trend is not implemented)
#' @return a character vector with the names of the selected variables.
#' @export
selectFromCompareGroups <- function(x, p.threshold = 0.2, which.p = "p.overall"){
  selectedvar <- c()
  
  if(which.p == "p.overall"){
    for (i in 1:length(x)) {
      if (!is.na(x[[i]]$p.overall)){
        if (x[[i]]$p.overall < p.threshold) selectedvar <- c(selectedvar, attributes(x)$varnames.orig[[i]])
      }
    }
  }
  
  if(which.p == "p.ratio"){
    for (i in 1:length(x)) {
      if (sum(1*!is.finite(as.numeric(attr(x[[i]], "p.ratio"))))<=1){
        if (min(as.numeric(attr(x[[i]], "p.ratio")), na.rm = TRUE) < p.threshold) selectedvar <- c(selectedvar, attributes(x)$varnames.orig[[i]])
      }
    }
  }
  
  return(selectedvar)
}