R/readFiles.R

In Yang0014/MassSpectrometry: Tools for Glyco Native Mass Spectrometry Analysis

### -----------------------------------------------------------------
### readMZ: read data from mz files
### Exported!
readMZ <- function(fns, scanCounts=NULL, starts=NULL, ends=NULL){
  if(is.null(scanCounts)){
    scanCounts <- sapply(fns, function(x){runInfo(openMSfile(x))$scanCount})
    if(length(unique(scanCounts)) > 1L){
      warning("Using different scanCounts number in files!")
    }
  }else{
    stopifnot(length(fns) == length(scanCounts))
  }
  pls <- mapply(function(x,y){
    aa <- openMSfile(x)
    ans <- peaks(aa, y)
  }, fns, scanCounts)
  
  ## Merge the peaks witin the start and end ranges
  if(!is.null(starts) && !is.null(ends)){
    stopifnot(length(starts) == length(ends))
    stopifnot(all(starts < ends))
    intensities <- matrix(nrow=length(pls), ncol=length(starts),
                          dimnames=list(names(pls), (starts+ends)/2))
    for(i in 1:length(pls)){
      pl <- pls[[i]]
      pl[ ,2] <- pl[ ,2] / max(pl[ ,2]) * 100
      intensities[i, ] <- mapply(function(start, end, pl)
        {sum(pl[pl[ ,1] >= start & pl[ ,1] <= end, 2])}, starts, ends,
        MoreArgs=list(pl))
    }
    return(as.data.frame(intensities))
  }
  return(pls)
}

readProteinDevolutionXls = function(xlsFn, sheet="Sheet1", chargeState){
  sheetData <- read_excel(xlsFn, sheet = sheet)
  indexMain = which(!is.na(sheetData[ ,"No.."]))
  resultSheet = sheetData[indexMain, ]
  #indexChargeState = which(sheetData[ ,"Average.Mass"] == chargeState)
  indexChargeState = rep(NA, nrow(resultSheet))
  j = 0
  for(i in 1:nrow(sheetData)){
    if(sheetData[i, "Average.Mass"] == "Charge State"){
      j = j + 1
    }
    if(sheetData[i, "Average.Mass"] == as.character(chargeState)){
      indexChargeState[j] = i
    }
  }
  measuredAverage = sheetData[indexChargeState, "Sum.Intensity"]
  stopifnot(length(measuredAverage) == nrow(resultSheet))
  resultSheet = cbind(resultSheet, "Measured Average m/z"=as.numeric(measuredAverage))
  resultSheet = as.data.frame(data.matrix(resultSheet))
  resultSheet = resultSheet[order(resultSheet[["Average.Mass"]]), ]
  return(resultSheet)
}

my.write.table = function(values, file=file, head="Identifier", row.names=TRUE, col.names=TRUE,
                          append=FALSE, quote=FALSE, sep="\t", na="NA", digits=NA){

  if (is.vector(values)){
    values = as.data.frame(values)
  }

  if (!is.na(digits)){
    if (is.data.frame(values)){
      for (i in 1:length(values)){
        if (is.numeric(values[[i]])){
          isInteger = as.integer(values[[i]]) == values[[i]]
          isInteger[is.na(isInteger)] = TRUE
          if (any(!isInteger)){
            values[[i]] = signif(values[[i]], digits=digits)
          }
        }
      }
    } else {
      if (is.numeric(values)){
        values = signif(values, digits=digits)
      }
    }
  }

  if (row.names){
    if (col.names){
      write.table(matrix(c(head, colnames(values)), nrow=1), file=file, sep=sep, quote=quote, col.names=FALSE, row.names=FALSE, append=append, na=na)
    }
    write.table(values, file=file, sep=sep, quote=quote, col.names=FALSE, row.names=TRUE, append=TRUE, na=na)
  } else {
    write.table(values, file=file, sep=sep, quote=quote, col.names=col.names, row.names=FALSE, append=append, na=na)
  }
}