# Why square root transformation and not log:
# Anal Bioanal Chem. 2011 Jul; 401(1): 167–181.
# Published online 2011 Apr 12. doi: 10.1007/s00216-011-4929-z
#"Especially for multivariate treatment of MALDI imaging data, the square root transformation can be considered for the data preparation
#because for all three intensity groups in Table 1, the variance is approximately constant."
#' processSmallMolSpectra
#'
#' @param input MALDIquant mass spectrum list
#'
#' @return MALDIquant mass spectrum list
#' @export
#'
processSmallMolSpectra <- function(input){
peaks <- MALDIquant::smoothIntensity(input,
method = "SavitzkyGolay",
halfWindowSize = 20)
peaks <- MALDIquant::removeBaseline(peaks,
method = "TopHat")
peaks <- MALDIquant::calibrateIntensity(peaks,
method = "TIC")
MALDIquant::detectPeaks(peaks,
method = "SuperSmoother",
halfWindowSize = 20,
SNR = 1)
}
#' processProteinSpectra
#'
#' @param input MALDIquant mass spectrum list
#'
#' @return MALDIquant mass spectrum list
#' @export
#'
processProteinSpectra <- function(input){
peaks <- MALDIquant::transformIntensity(input,
method = "sqrt")
peaks <- MALDIquant::smoothIntensity(peaks,
method = "SavitzkyGolay",
halfWindowSize = 20)
peaks <- MALDIquant::removeBaseline(peaks,
method = "TopHat")
peaks <- MALDIquant::detectPeaks(peaks,
method = "MAD",
halfWindowSize = 20,
SNR = 3)
lapply(peaks,
function(x){
x@intensity <- x@intensity * (100/max(x@intensity))
x
})
}
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