R/proteinPeaksToMatrix.r

In chasemc/tempRepo: Protein and small molecule analysis of bacteria by MALDI-TOF MS

#' proteinPeaksToMatrix
#'
#' @param bool NA
#' @param proteinPeaks NA
#'
#' @return NA
#' @export
#'

proteinPeaksToMatrix <- function(bool, proteinPeaks){
  
  
  temp <- NULL
  for (i in 1:length(proteinPeaks)) {
    temp <- c(temp, proteinPeaks[[i]]@metaData$Strain)
  }
  proteinSamples <- factor(temp)
  proteinMatrixInnard <- MALDIquant::intensityMatrix(proteinPeaks)
  rownames(proteinMatrixInnard) <- paste(proteinSamples)
  proteinMatrixInnard[is.na(proteinMatrixInnard)] <- 0
  
  if(bool == "0"){
    proteinMatrixInnard
  }else if (bool == "1") {
    ifelse(proteinMatrixInnard > 0, 1, 0)
    
  }else{
    proteinMatrixInnard
  }
  
}