R/getESDC.R

In classSNitch: Classifies RNA Structure Change in Chemical Mapping Data

#' A function to get experimental structure disruption coefficient (eSDC).
#' @title getESDC
#' @aliases getESDC
#' @keywords trace eSDC RNA
#' @usage getESDC(sample, base=sample[1,], margin=1)
#' @param sample A numeric matrix containing values to be compared (e.g. a set of mutant SHAPE traces).
#' @param base An optional numeric vector containing the values to which the samples are to be compared (e.g. a wildtype SHAPE trace). Default is the first trace in sample.
#' @param margin An optional number indicating if the samples are organized by rows or columns, where 1 indicates rows and 2 indicates columns. Default is 1.
#' @export
#' @details This function calculates the eSDC between the base vector and each row (or column) in sample.
#' @return A numeric vector of eSDC values.
#' @author Chanin Tolson
#' @seealso  \code{\link{getFeatures}} 
#' @examples #sample data
#' sample = matrix(sample(1:100), ncol=10)
#' #normalize
#' samp_norm = normalize(sample)
#' #reduce noise
#' samp_nreduce = reduceNoise(samp_norm, trim=1, high=4)
#' #get trace difference
#' eSDC = getESDC(samp_nreduce)
getESDC = function(sample, base=sample[1,], margin=1){
  
  #set optional paramater margin
  if(missing(margin)) {
    margin = 1
  } else {
    if(!(margin %in% c(1,2))){
      warning("Margin value not valid. Margin set to default.")
      margin = 1
    }
    if(margin==2){
      sample = t(sample)
    }
  }
  
  #set optional paramater base
  if(missing(base)) {
    base = sample[1,]
  } else {    
    base = base
  }
  
  #calculate eSDC
  if(dim(sample)[1]==1){
    eSDC = (1-cor(as.vector(sample), base, method="pearson", use="pairwise.complete.obs"))/sqrt(length(sample))
  } else{
    eSDC = (1-apply(sample, 1, cor, x=base, method="pearson", use="pairwise.complete.obs"))/sqrt(ncol(sample))
  }
  
  #return eSDC
  return(eSDC)
}