R/list.responses.continuous.multi.R

In antagomir/netresponse: Functional Network Analysis

#' @title Investigate association of a continuous variable and the modes
#' @description Investigate association of a continuous variable and the modes given a list of groupings
#' @param annotation.df annotation data.frame with discrete factor levels, rows
#' named by the samples
#' @param groupings Sample mode information. Each element corresponds to one grouping; each grouping lists samples for the modes within that grouping.
#' @param method method for quantifying the association
#' @param pth p-value threshold applied to adjusted p-values
#' @param verbose verbose 
#' @param rounding rounding digits
#' @return Table listing all associations between the factor levels and responses
#' @author Contact: Leo Lahti \email{leo.lahti@@iki.fi}
#' @references See citation('netresponse')
#' @export
#' @importFrom qvalue qvalue
#' @keywords utilities
#' @examples res <- list.responses.continuous.multi(annotation.df = NULL, groupings = NULL)
list.responses.continuous.multi <- function(annotation.df, groupings, method = "t-test", 
    pth = Inf, verbose = TRUE, rounding = NULL) {

    if (is.null(groupings)) {return(NULL)}

    # annotation.df <- annot[, continuous.vars]; groupings <- groupings.listing; pth
    # = pth; method <- 't-test'; verbose = TRUE; rounding = NULL
    
    tab <- NULL
    for (gn in names(groupings)) {
        
        gntab <- list.responses.continuous.single(annotation.df, groupings[[gn]], 
            method = method, pth = Inf, verbose = verbose, rounding = rounding, adjust.p = FALSE)
        
        gntab <- cbind(grouping = gn, gntab)
        tab <- rbind(tab, gntab)
        
    }
    
    tab$p.adj <- rep(NA, nrow(tab))
    if (nrow(tab) > 100) {
        qv <- qvalue(tab$pvalue, pi0.method = "bootstrap", fdr.level = 0.25)
        if (("qvalues" %in% names(qv))) {
            tab$p.adj <- qv$qvalues
        }
    } else {
        tab$p.adj <- p.adjust(tab$pvalue, method = "BH")
    }
    
    tab$pvalue <- NULL
    tab <- tab[tab$p.adj < pth, ]
    
    tab
    
}