OptiREF_raw/InterCategoryVar.R at master · EvaFro/OptiREF_raw · GitHub

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##InterCategoryVar.R ##
#' @export
#'

##############################################
## Author Information ##

# * Author: E.Frolli
# * Orginization: Univeristy of Texas Marine Science Institute
# * Contact: frolli.erin@utexas.edu
# * Date: 26 Jun 2017


##############################################
## The Code ##

InterCategoryVar <-function(qPCRData,Category) {

  # Matrix vals
  n = nrow(qPCRData) # Number of rows
  L = ncol(qPCRData) # Number of col
  GeneSymbol = colnames(qPCRData) # Gene Symbols

  # Category info
  CategoryNum = as.numeric(summary.factor(Category)) # total number of samples for each Category
  CategoryName = levels(Category) # unique Category names
  CategoryL = length(CategoryNum) # total number of Categorys for dataset

  # Gene Averages / Category/ sample
  Zig. = matrix(0,CategoryL,L)

  for(i in 1:CategoryL){
    Zig.[i,] = apply(qPCRData[Category==CategoryName[i],],2,mean) # average of each gene by Category
  }

  # Sample Average of Genes
  Zj.=apply(Zig.,2,mean)

  # Category Average of Genes
  Z.g=apply(Zig.,1,mean)

  # Overall Average of Genes
  Z..=mean(Zig.)

  # Calculate difference dig = Zig. - Zj. - Z.g + Z..

  dig = matrix(0,CategoryL,L)

  for(i in 1:L){
    for (ii in 1:CategoryL){
      dig[ii,i] = Zig.[ii,i]- Zj.[i] - Z.g[ii] + Z..  # Equation on page 4 in sumplemental material for Andersen et al.
    }
  }

  colnames(dig) = GeneSymbol
  rownames(dig) = CategoryName

  # Difference between the Categorys per gene: di = 2*max(abs(dig))
  di = 2*apply(abs(dig),2,max)

  # return these values.
    return(list("dig"=dig,"di"=di))
}