R/mIFTO.welch.t.test.calculations.R

In AstroPathJHU/mIFTO: mIFTO: Multiplex Immunoflourescence Titration Optimization

#########################welch.t.test.calculations##############################
#
#'Used by analysis functions to do the T-Test calculations
#'
#'T.Test.Calculations;
#'Created By: Benjamin Green;
#'Last Edited 09/27/2019
#'
#'Takes in the data and some constants from the PixelbyPixel script and
#'returns a T test for postive and negative
#'Signal defined by the threshold
#'
#' @param positivity.data a list of four images, positive,
#'   negative values then positive, negative binary image masks
#' @param Concentration is a numeric vector of the denominator of all
#' concentration ratios
#'  which a boxplot will be created for (ie 25, 50, 100)
#' @param x is the slide ID
#' @param q is image id
#' @return a list with two data.frames; one with a t test for shift factor of
#' log(x+1) and one with a shift factor of log(x+.001)
#' the data.frames hold two columns one for the t test value and one for the
#' concentration of interest
#' @export
#'
mIFTO.welch.t.test.calculations<-function(positivity.data,Concentration,x,q){
  export_var <- function(v1) {
    filename = paste0("C:\\Users\\Public\\Documents\\", deparse(substitute(v1)), ".csv")
    write.csv(v1, filename, row.names=FALSE)
  }
  #
  epsilon<-c(1,.001)
  #
  out<-vector('list',length(epsilon))
  save.image(file = "C:\\Users\\Public\\Documents\\positivitydata.RData")
  for(epsilon.count in 1:length(epsilon)){
    #
    Signal <- positivity.data[['pos']]
    # export_var(Signal)
    Signal.mask <- positivity.data[['pos.mask']]
    # export_var(Signal.mask)
    SignalOnly <- Signal[positivity.data[['pos.mask']] == 1]
    SignalOnly <- log(SignalOnly + epsilon[epsilon.count])
    #
    Noise <- positivity.data[['neg']]
    # export_var(Noise)
    Noise.mask <- positivity.data[['neg.mask']]
    # export_var(Noise.mask)
    NoiseOnly <- Noise[positivity.data[['neg.mask']] == 1]
    NoiseOnly <- log(NoiseOnly + epsilon[epsilon.count])
    #
    if(length(SignalOnly)<5){

      out[[epsilon.count]] <-cbind.data.frame(
        statistic = 0,
        Concentration = Concentration,
        Slide.ID = x,
        Image.ID = q)

    }else{

      out[[epsilon.count]] <-cbind.data.frame(
          t.test(
            SignalOnly,NoiseOnly)['statistic'],
        Concentration=Concentration,
        Slide.ID = x,
        Image.ID = q)
    }}

  names(out)<-c('Plus1','Plus001')
  out
  #
  }