R/DataProcessing.R

In LinkHD: LinkHD: a versatile framework to explore and integrate heterogeneous data

#' @title DataProcessing
#' @description  function to Perform external datas' pre-processing.
#' This function allows an external pre-processing of the datasets including on the analysis in three ways: Standard, Compositional (centered log ratio) and
#' frequencies.
#'
#' @param Data a numeric data.frame.
#' @param Method character indicating the method used to Data preprocessing. If data are continous, use 'Standard'.
#' If Data are compositional, please use 'Compositional' and clr (centered log-ratios functions) transformations are performed.
#' To compositional data, you also could use the option 'TSS' Total Sum Scaling follow up bray (Bray-Curtis) in distance option.
#' The function also allows to processing frequencies- like data through 'FreqNorm' option.
#' Note that when you use Compositional, we first sum 1 to all the counts (in order to performs the log transformation before).
#' @return a data.frame with normalized data.
#' @export DataProcessing
#' @author Laura M Zingatetti
#'
#'
#' @examples
#' {
#' data(Taraoceans)
#' Data<-Taraoceans$phychem
#' Data<-DataProcessing(Data,Method='Standard')
#' }
# 

DataProcessing <- function(Data = NULL, Method = "Standard") {
    
    if (is.null(Data)) {
        stop("You should include a data.frame to standarized")
    }
    
    if (Method != "Standard" & Method != "Compositional" & Method != "FreqNorm" & Method != "TSS") {
        stop("You have to choose a valid Method to data standarization")
    }
    
    if (Method == "Standard") {
        Data <- scale(Data, scale = TRUE, center = TRUE)
    }
    
    
    if (Method == "FreqNorm") {
        Data <- cia(Data)
    }
    
    if (Method == "Compositional") {
        Data <- centerLR(Data + 1)$Data.clr
    }
    
    if (Method == "TSS") {
        Data <- t(apply(Data + 1, 1, TSSfunction))
    }
    
    return(Data)
}