R/calcSummary.R

In BEclear: Correction of batch effects in DNA methylation data

#' calcSummary
#'
#' @aliases calcSummary
#'
#' @title Summarize median comparison and p-value calculation results
#'
#' @seealso \code{\link{calcBatchEffects}}
#' @seealso \code{\link{correctBatchEffect}}
#'
#' @description  Summarizes the results of the \code{\link{calcBatchEffects}} 
#' function
#'
#' @details All genes with a median comparison value >= 0.05 and a p-value
#' of <= 0.01 are summarized into a data.frame. These genes are assumed to
#' contain a batch effect
#'
#' @param medians a matrix containing median difference values calculated by
#' the \code{\link{calcBatchEffects}} function. For further details look at the
#' documentation of this function.
#' @param pvalues a matrix containing p-values calculated by the
#' \code{\link{calcBatchEffects}} function. For further details look at the
#' documentation of this function.
#' @param mediansTreshold the threshold above or equal median values are regarded 
#' as batch effected, when the criteria for p-values is also met.
#' @param pvaluesTreshold the threshold below or equal p-values are regarded as 
#' batch effected, when the criteria for medians is also met.
#'
#' @export calcSummary
#' @importFrom abind abind
#' @importFrom futile.logger flog.info
#' @import data.table
#' @usage calcSummary(medians, pvalues, mediansTreshold, pvaluesTreshold)
#'
#' @return Null if there are no batch effects detected, else
#' a \code{\link[data.table]{data.table}} with the columns "gene" containing the gene name,
#' "batch" containing the batch number from which the gene was found, "median"
#' and "p-value" containing the calculated median difference values and the
#' p-values, respectively.
#'
#' @examples
#' ## Shortly running example. For a more realistic example that takes
#' ## some more time, run the same procedure with the full BEclearData
#' ## dataset.
#' 
#' ## Whole procedure that has to be done to use this function.
#' data(BEclearData)
#' ex.data <- ex.data[31:90, 7:26]
#' ex.samples <- ex.samples[7:26, ]
#' 
#' ## Calculate the batch effects
#' batchEffects <- calcBatchEffects(data = ex.data, samples = ex.samples,
#' adjusted = TRUE, method = "fdr")
#' med <- batchEffects$med
#' pvals <- batchEffects$pval
#' 
#' ## Summarize p-values and median differences for batch affected genes
#' sum <- calcSummary(medians = med, pvalues = pvals)
calcSummary <- function(medians, pvalues, mediansTreshold = 0.05, 
                        pvaluesTreshold = 0.01) {
    
    flog.info("Generating a summary table")
    x <- abind(medians, pvalues, along = 3)
    ## find affected genes
    affected <- apply(x, c(1,2), FUN = 
                          function(X){ return((is.na(X[1]) |  X[1] >= mediansTreshold) 
                                   & X[2] <= pvaluesTreshold)})
    
    if(sum(affected) == 0){
        return(NULL)
    }else{
        tmp <- arrayInd(which(affected), dim(affected))
        
        return(data.table(gene = rownames(medians)[tmp[,1]],
                          batch_id = colnames(medians)[tmp[,2]],
                          median = medians[affected], 
                          pvalue = pvalues[affected]))
    }
}