R/reshape.DEswan.R

In lehallib/DEswan: Differential Expression Sliding Window ANalaysis

#' Reshape DE-SWAN output
#'
#' @param 
#' res.DEswan: a data Frame - output from DEswan
#' @param 
#' parameter: an optional numeric - 1 for pvalue or 2 for coefficients. Default is 1
#' @param 
#' factor: an optional character string - qt or covariates in DEswan. Default is qt.
#' @export
#' @examples
#' res.DEswan=DEswan(data.df = agingplasmaproteome[,-c(1:3)],
#' qt = agingplasmaproteome[,1],
#' window.center = seq(40,100,10),
#' buckets.size = 10,
#' covariates = agingplasmaproteome[,c(2:3)])
#' head(res.DEswan$p)
#' head(res.DEswan$coeff)
#' res.DEswan.wide.p=reshape.DEswan(res.DEswan)
#' res.DEswan.wide.p=reshape.DEswan(res.DEswan,parameter = 1,factor = "qt")
#' head(res.DEswan.wide.p)
#' res.DEswan.wide.coeff=reshape.DEswan(res.DEswan,parameter = 2,factor = "qt")
#' head(res.DEswan.wide.coeff)

reshape.DEswan=function(res.DEswan, parameter, factor){
  
  if(missing(res.DEswan)==T){
    print("No input DEswan results")
    stop
  }
  if(missing(parameter)==T){
    parameter=1
  }
  if(missing(factor)==T){
    factor = "qt"
  }


  
  toReshape=res.DEswan[[parameter]]
  # head(toReshape)
  toReshape=toReshape[which(toReshape$factor==factor),-3]
  res.DEswan.wide=data.frame(reshape::cast(toReshape,variable~window.center,value = colnames(toReshape)[3]),stringsAsFactors = F)
  return(res.DEswan.wide)
}