R/Params_db.R
In xia-lab/OptiLCMS: Optimized LC-MS Spectra Processing
Defines functions
SetPeakParam
Documented in
SetPeakParam
# Parameter Function
#' @title Set parameters for peak profiling and parameters optimization
#' @description This function sets all the parameters used for downstream
#' pre-processing of user's raw MS data based on specific Liquid chromatography–mass spectrometry (LC-MS)
#' platform or parameters optimization.
#' The database will be under an real-time update based on the progress in this field.
#'
#' @param platform Character, specify the LC-MS platform used in pratice, including "UPLC-Q/E",
#' "UPLC-Q/TOF","UPLC-T/TOF","UPLC-Ion_Trap","UPLC-Orbitrap","UPLC-G2S","HPLC-Q/TOF","HPLC-Ion_Trap","HPLC-Orbitrap","HPLC-S/Q".
#' Default is "general", which is a more common option for all platform. If the platform is not listed above, please use this one.
#' @param Peak_method Character, specify the algorithm to perform peak detection. "centwave"
#' to use the CentWave algorithm, and "matchedFilter" to use the MatchedFilter algorithm.
#' @param RT_method Character, specify the algorithm to perform tetention time alignment, including "loess" and "obiwarp".
#' Default is "loess".
#' @param ppm Numeric, specify the mass error in ppm.
#' @param min_peakwidth Numeric, specify the minimum peak width in seconds.Only work for 'centWave'.
#' @param max_peakwidth Numeric, specify the maximum peak width in seconds.Only work for 'centWave'.
#' @param snthresh Numeric, specify the signal to noise threshold. Work for both 'centwave' and 'matchedFilter'.
#' @param mzdiff Numeric, specify the minimum m/z difference for signals to be considered as
#' different features when retention times are overlapping.
#' @param bw Numeric, specify the band width (sd or half width at half maximum) of gaussian
#' smoothing kernel to be applied during peak grouping.
#' @param noise Numeric, specify the noise level for peaking picking.Only work for 'centWave'.
#' @param prefilter Numeric, specify the scan number threshold for prefilter.Only work for 'centWave'.
#' @param value_of_prefilter Numeric, specify the scan abundance threshold for prefilter. Only work for 'centWave'.
#' @param peakBinSize Numeric, specifying the width of the bins/slices in m/z dimension. Only work for 'matchedFilter'.
#' @param fwhm numeric specifying the full width at half maximum of matched filtration gaussian model peak. Only work for 'matchedFilter'.
#' @param steps numeric defining the number of bins to be merged before filtration. Only work for 'matchedFilter'.
#' @param sigma numeric specifying the standard deviation (width) of the matched filtration model peak. Only work for 'matchedFilter'.
#' @param max numeric, representing the maximum number of peaks that are expected/will be identified per slice. Only work for 'matchedFilter'.
#' @param profStep numeric defining the bin size (in mz dimension) to be used for the profile matrix generation. Only work for 'obiwarp'.
#' @param minFraction Numeric, specify fraction of samples in each group that contain the feature for it to be grouped.
#' @param minSamples Numeric, specify minimum number of sample(s) in each group that contain the feature for it to be included.
#' @param maxFeatures Numeric, specify the maximum number of features to be identified.
#' @param extra Numeric, defining the maximal number of additional peaks for all samples to be assigned to a peak group (i.e. feature) for retention time correction
#' @param span Numeric, defining the degree of smoothing (if smooth = "loess"). This parameter is passed to the internal call to loess
#' @param smooth Character, defining the function to be used, to interpolate corrected retention times for all peak groups. Either "loess" or "linear".
#' @param family Character, defining the method to be used for loess smoothing. Allowed values are "gaussian" and "symmetric"
#' @param fitgauss Logical, whether or not a Gaussian should be fitted to each peak. This affects mostly the retention time position of the peak.
#' @param mzCenterFun Character, Name of the function to calculate the m/z center of the chromatographic peak.
#' @param integrate Integration method. For integrate = 1 peak limits are found through descent on the mexican hat filtered data, for integrate = 2 the descent is done on the real data. The latter method is more accurate but prone to noise, while the former is more robust, but less exact.
#' @param polarity PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param perc_fwhm PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param mz_abs_iso PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param max_charge PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param max_iso PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param corr_eic_th PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param mz_abs_add PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param adducts PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param rmConts Logical, specify whether to exclude/remove the potential contaminations (the ones with RT range over 50% of the whole spetra).
#' @param BlankSub Logical, to substract blanks samples or not
#' @param criticalValue criticalValue for massifquant (supported later).
#' @param consecMissedLimit consecMissedLimit for massifquant (supported later).
#' @param unions unions for massifquant (supported later).
#' @param checkBack checkBack for massifquant (supported later).
#' @param withWave withWave for massifquant (supported later).
#' need to change.
#' @author Zhiqiang Pang \email{zhiqiang.pang@mail.mcgill.ca}, Jasmine Chong \email{jasmine.chong@mail.mcgill.ca}, and Jeff Xia \email{jeff.xia@mcgill.ca}
#' McGill University, Canada
#' License: GNU GPL (>= 2)
#' @import utils
#' @export
#' @return will return a peak processing parameters' set
#' @references Smith, C.A. et al. 2006. {Analytical Chemistry}, 78, 779-787
#' @examples
#' params <- SetPeakParam(platform = "UPLC-Q/E")
SetPeakParam <- function(platform = "general", Peak_method = "centWave", RT_method = "loess",
mzdiff, snthresh, bw, # used for both "centwave" and "matchedFilter"
ppm, min_peakwidth, max_peakwidth, noise, prefilter, value_of_prefilter, # used for "centwave"
fwhm, steps, sigma, peakBinSize, max, # used for "matchedFilter"
criticalValue, consecMissedLimit, unions, checkBack, withWave, # used for "massifquant"
profStep, # used for "obiwarp"
minFraction, minSamples, maxFeatures, mzCenterFun, integrate,# used for grouping
extra, span, smooth, family, fitgauss, # used for RT correction with peakgroup "loess"
polarity, perc_fwhm, mz_abs_iso, max_charge, max_iso, corr_eic_th, mz_abs_add, adducts, #used for annotation
rmConts, BlankSub #used to control remove contamination or not
) {
if(!exists(".SwapEnv")){
.SwapEnv <<- new.env(parent = .GlobalEnv);
.SwapEnv$.optimize_switch <- FALSE;
.SwapEnv$count_current_sample <- 0;
.SwapEnv$count_total_sample <- 120; # maximum number for on.public.web
.SwapEnv$envir <- new.env();
}
if (.on.public.web() & missing(platform) & missing(Peak_method) & file.exists("params.rda")){
#marker_record(paste0("operators","_operators_1"));
load("params.rda");
if(!.SwapEnv$.optimize_switch){
print_mes <- "\nStep 2/6: Internalize parameters! \nThis step will be finished soon...";
write.table(print_mes,file="metaboanalyst_spec_proc.txt",append = TRUE,row.names = FALSE,col.names = FALSE, quote = FALSE, eol = "\n");
print_mes <- "Step 2/6: Parameters Internalized Successfully! \nGoing to the next step...";
write.table(print_mes,file="metaboanalyst_spec_proc.txt",append = TRUE,row.names = FALSE,col.names = FALSE, quote = FALSE, eol = "\n");
write.table(unlist(peakParams),file="param_default.txt",row.names = TRUE,col.names = FALSE,quote = FALSE);
}
return(peakParams);
}
peakParams <- list()
if (missing(platform)){
platform<-"general"
} else{
match.arg(arg = platform ,choices = c("general","UPLC-Q/E","UPLC-Q/TOF","UPLC-T/TOF",
"UPLC-Ion_Trap","UPLC-Orbitrap","UPLC-G2S",
"HPLC-Q/TOF","HPLC-Ion_Trap","HPLC-Orbitrap",
"HPLC-S/Q"))
}
### Platform Selection--UPLC----
if (platform=="UPLC-Q/E"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 5;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 20;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 4;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 0;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 10;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="UPLC-Q/TOF"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 15;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 20;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 6;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="UPLC-T/TOF"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 15;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 20;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 6;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 0;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="UPLC-Ion_Trap"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 50;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 20;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 4;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 0;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="UPLC-Orbitrap"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 2.5;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 20;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 5000;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="UPLC-G2S"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 15;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 2;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 25;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 500;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 0.5;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
### Platform Selection--HPLC----
if (platform=="HPLC-Q/TOF"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 30;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 10;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 60;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 6;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 500;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="HPLC-Ion_Trap"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 50;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 10;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 60;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 6;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="HPLC-Orbitrap"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 3;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 10;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 60;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 6;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="HPLC-S/Q"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 30;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 10;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 60;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 6;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
### Platform Selection--OTHERS-General---
if (platform=="general"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 5;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 30;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="Massifquant"){
if (missing(ppm)){
peakParams$ppm <- 5;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 30;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
if (missing(criticalValue)){
peakParams$criticalValue <- 1.125;
} else{
peakParams$criticalValue <- criticalValue;
};
if (missing(consecMissedLimit)){
peakParams$consecMissedLimit <- 2;
} else{
peakParams$consecMissedLimit <- consecMissedLimit;
};
if (missing(unions)){
peakParams$unions <- 1;
} else{
peakParams$unions <- unions;
};
if (missing(checkBack)){
peakParams$checkBack <- 0;
} else{
peakParams$checkBack <- checkBack;
};
if (missing(withWave)){
peakParams$withWave <- FALSE;
} else{
peakParams$withWave <- withWave;
};
};
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 10;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
# if (missing(verbose.columns)){
peakParams$verbose.columns <- FALSE;
# } else{
# peakParams$verbose.columns <- verbose.columns
# };
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
## Generic Params
# if (missing(verbose.columns)){
peakParams$verbose.columns <- FALSE;
# } else{
# peakParams$verbose.columns <- verbose.columns
# };
### Platform Selection--OTHERS-Annotation---
### Setup Peak Annotation Parameters
if("annotation" =="annotation"){
# TO DO: add more annotation in future
if (missing(polarity)){
peakParams$polarity <- "negative";
} else{
peakParams$polarity <- polarity;
}
if (missing(perc_fwhm)){
peakParams$perc_fwhm <- 0.6;
} else{
peakParams$perc_fwhm <- perc_fwhm;
}
if (missing(mz_abs_iso)){
peakParams$mz_abs_iso <- 0.005;
} else{
peakParams$mz_abs_iso <- mz_abs_iso;
}
if (missing(max_charge)){
peakParams$max_charge <- 2;
} else{
peakParams$max_charge <- max_charge;
}
if (missing(max_iso)){
peakParams$max_iso <- 2;
} else{
peakParams$max_iso <- max_iso;
}
if (missing(corr_eic_th)){
peakParams$corr_eic_th <- 0.85;
} else{
peakParams$corr_eic_th <- corr_eic_th;
}
if (missing(mz_abs_add)){
peakParams$mz_abs_add <- 0.001;
} else{
peakParams$mz_abs_add <- mz_abs_add;
}
if (missing(adducts)){
peakParams$adducts <- NULL;
} else{
peakParams$adducts <- adducts;
}
}
# Set potential Contaminats removal (rmConts) or not
if(missing(rmConts)){
peakParams$rmConts <- TRUE;
} else {
peakParams$rmConts <- as.logical(rmConts);
}
# Set potential Contaminats removal (rmConts) or not
if(missing(BlankSub)){
peakParams$BlankSub <- TRUE;
} else {
peakParams$BlankSub <- as.logical(BlankSub);
}
#Output a table for display
if(.on.public.web()){
if(file.exists("params.rda")){
file.rename("params.rda", "params_last.rda")
}
save(peakParams,file="params.rda");
write.table(unlist(peakParams),file="param_default.txt",row.names = TRUE,col.names = FALSE,quote = FALSE);
write.table("NOT Finished Yet!",file="param_optimized.txt",row.names = TRUE,col.names = FALSE,quote = FALSE);
}
#### Other Parameters
# None for now !
return(peakParams)
}
xia-lab/OptiLCMS documentation built on Nov. 6, 2024, 11:01 a.m.
R Package Documentation
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Defines functions SetPeakParam
Documented in SetPeakParam
# Parameter Function
#' @title Set parameters for peak profiling and parameters optimization
#' @description This function sets all the parameters used for downstream
#' pre-processing of user's raw MS data based on specific Liquid chromatography–mass spectrometry (LC-MS)
#' platform or parameters optimization.
#' The database will be under an real-time update based on the progress in this field.
#'
#' @param platform Character, specify the LC-MS platform used in pratice, including "UPLC-Q/E",
#' "UPLC-Q/TOF","UPLC-T/TOF","UPLC-Ion_Trap","UPLC-Orbitrap","UPLC-G2S","HPLC-Q/TOF","HPLC-Ion_Trap","HPLC-Orbitrap","HPLC-S/Q".
#' Default is "general", which is a more common option for all platform. If the platform is not listed above, please use this one.
#' @param Peak_method Character, specify the algorithm to perform peak detection. "centwave"
#' to use the CentWave algorithm, and "matchedFilter" to use the MatchedFilter algorithm.
#' @param RT_method Character, specify the algorithm to perform tetention time alignment, including "loess" and "obiwarp".
#' Default is "loess".
#' @param ppm Numeric, specify the mass error in ppm.
#' @param min_peakwidth Numeric, specify the minimum peak width in seconds.Only work for 'centWave'.
#' @param max_peakwidth Numeric, specify the maximum peak width in seconds.Only work for 'centWave'.
#' @param snthresh Numeric, specify the signal to noise threshold. Work for both 'centwave' and 'matchedFilter'.
#' @param mzdiff Numeric, specify the minimum m/z difference for signals to be considered as
#' different features when retention times are overlapping.
#' @param bw Numeric, specify the band width (sd or half width at half maximum) of gaussian
#' smoothing kernel to be applied during peak grouping.
#' @param noise Numeric, specify the noise level for peaking picking.Only work for 'centWave'.
#' @param prefilter Numeric, specify the scan number threshold for prefilter.Only work for 'centWave'.
#' @param value_of_prefilter Numeric, specify the scan abundance threshold for prefilter. Only work for 'centWave'.
#' @param peakBinSize Numeric, specifying the width of the bins/slices in m/z dimension. Only work for 'matchedFilter'.
#' @param fwhm numeric specifying the full width at half maximum of matched filtration gaussian model peak. Only work for 'matchedFilter'.
#' @param steps numeric defining the number of bins to be merged before filtration. Only work for 'matchedFilter'.
#' @param sigma numeric specifying the standard deviation (width) of the matched filtration model peak. Only work for 'matchedFilter'.
#' @param max numeric, representing the maximum number of peaks that are expected/will be identified per slice. Only work for 'matchedFilter'.
#' @param profStep numeric defining the bin size (in mz dimension) to be used for the profile matrix generation. Only work for 'obiwarp'.
#' @param minFraction Numeric, specify fraction of samples in each group that contain the feature for it to be grouped.
#' @param minSamples Numeric, specify minimum number of sample(s) in each group that contain the feature for it to be included.
#' @param maxFeatures Numeric, specify the maximum number of features to be identified.
#' @param extra Numeric, defining the maximal number of additional peaks for all samples to be assigned to a peak group (i.e. feature) for retention time correction
#' @param span Numeric, defining the degree of smoothing (if smooth = "loess"). This parameter is passed to the internal call to loess
#' @param smooth Character, defining the function to be used, to interpolate corrected retention times for all peak groups. Either "loess" or "linear".
#' @param family Character, defining the method to be used for loess smoothing. Allowed values are "gaussian" and "symmetric"
#' @param fitgauss Logical, whether or not a Gaussian should be fitted to each peak. This affects mostly the retention time position of the peak.
#' @param mzCenterFun Character, Name of the function to calculate the m/z center of the chromatographic peak.
#' @param integrate Integration method. For integrate = 1 peak limits are found through descent on the mexican hat filtered data, for integrate = 2 the descent is done on the real data. The latter method is more accurate but prone to noise, while the former is more robust, but less exact.
#' @param polarity PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param perc_fwhm PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param mz_abs_iso PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param max_charge PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param max_iso PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param corr_eic_th PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param mz_abs_add PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param adducts PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
#' @param rmConts Logical, specify whether to exclude/remove the potential contaminations (the ones with RT range over 50% of the whole spetra).
#' @param BlankSub Logical, to substract blanks samples or not
#' @param criticalValue criticalValue for massifquant (supported later).
#' @param consecMissedLimit consecMissedLimit for massifquant (supported later).
#' @param unions unions for massifquant (supported later).
#' @param checkBack checkBack for massifquant (supported later).
#' @param withWave withWave for massifquant (supported later).
#' need to change.
#' @author Zhiqiang Pang \email{zhiqiang.pang@mail.mcgill.ca}, Jasmine Chong \email{jasmine.chong@mail.mcgill.ca}, and Jeff Xia \email{jeff.xia@mcgill.ca}
#' McGill University, Canada
#' License: GNU GPL (>= 2)
#' @import utils
#' @export
#' @return will return a peak processing parameters' set
#' @references Smith, C.A. et al. 2006. {Analytical Chemistry}, 78, 779-787
#' @examples
#' params <- SetPeakParam(platform = "UPLC-Q/E")
SetPeakParam <- function(platform = "general", Peak_method = "centWave", RT_method = "loess",
mzdiff, snthresh, bw, # used for both "centwave" and "matchedFilter"
ppm, min_peakwidth, max_peakwidth, noise, prefilter, value_of_prefilter, # used for "centwave"
fwhm, steps, sigma, peakBinSize, max, # used for "matchedFilter"
criticalValue, consecMissedLimit, unions, checkBack, withWave, # used for "massifquant"
profStep, # used for "obiwarp"
minFraction, minSamples, maxFeatures, mzCenterFun, integrate,# used for grouping
extra, span, smooth, family, fitgauss, # used for RT correction with peakgroup "loess"
polarity, perc_fwhm, mz_abs_iso, max_charge, max_iso, corr_eic_th, mz_abs_add, adducts, #used for annotation
rmConts, BlankSub #used to control remove contamination or not
) {
if(!exists(".SwapEnv")){
.SwapEnv <<- new.env(parent = .GlobalEnv);
.SwapEnv$.optimize_switch <- FALSE;
.SwapEnv$count_current_sample <- 0;
.SwapEnv$count_total_sample <- 120; # maximum number for on.public.web
.SwapEnv$envir <- new.env();
}
if (.on.public.web() & missing(platform) & missing(Peak_method) & file.exists("params.rda")){
#marker_record(paste0("operators","_operators_1"));
load("params.rda");
if(!.SwapEnv$.optimize_switch){
print_mes <- "\nStep 2/6: Internalize parameters! \nThis step will be finished soon...";
write.table(print_mes,file="metaboanalyst_spec_proc.txt",append = TRUE,row.names = FALSE,col.names = FALSE, quote = FALSE, eol = "\n");
print_mes <- "Step 2/6: Parameters Internalized Successfully! \nGoing to the next step...";
write.table(print_mes,file="metaboanalyst_spec_proc.txt",append = TRUE,row.names = FALSE,col.names = FALSE, quote = FALSE, eol = "\n");
write.table(unlist(peakParams),file="param_default.txt",row.names = TRUE,col.names = FALSE,quote = FALSE);
}
return(peakParams);
}
peakParams <- list()
if (missing(platform)){
platform<-"general"
} else{
match.arg(arg = platform ,choices = c("general","UPLC-Q/E","UPLC-Q/TOF","UPLC-T/TOF",
"UPLC-Ion_Trap","UPLC-Orbitrap","UPLC-G2S",
"HPLC-Q/TOF","HPLC-Ion_Trap","HPLC-Orbitrap",
"HPLC-S/Q"))
}
### Platform Selection--UPLC----
if (platform=="UPLC-Q/E"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 5;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 20;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 4;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 0;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 10;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="UPLC-Q/TOF"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 15;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 20;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 6;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="UPLC-T/TOF"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 15;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 20;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 6;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 0;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="UPLC-Ion_Trap"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 50;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 20;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 4;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 0;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="UPLC-Orbitrap"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 2.5;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 20;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 5000;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="UPLC-G2S"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 15;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 2;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 25;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 500;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 0.5;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
### Platform Selection--HPLC----
if (platform=="HPLC-Q/TOF"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 30;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 10;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 60;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 6;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 500;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="HPLC-Ion_Trap"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 50;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 10;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 60;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 6;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="HPLC-Orbitrap"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 3;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 10;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 60;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 6;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
if (platform=="HPLC-S/Q"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 30;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 10;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 60;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 6;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 30;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
### Platform Selection--OTHERS-General---
if (platform=="general"){
if (missing(Peak_method)){
peakParams$Peak_method <- "centWave"
} else{
peakParams$Peak_method <- Peak_method;
};
if (missing(RT_method)){
peakParams$RT_method <- "loess"
} else{
peakParams$RT_method <- RT_method;
};
## Parameters for Peakpicking
if (Peak_method=="centWave" | Peak_method=="null"){ peakParams$Peak_method="centWave";
if (missing(ppm)){
peakParams$ppm <- 5;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 30;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
}
if (Peak_method=="Massifquant"){
if (missing(ppm)){
peakParams$ppm <- 5;
} else{
peakParams$ppm <- ppm;
};
if (missing(min_peakwidth)){
peakParams$min_peakwidth <- 5;
} else{
peakParams$min_peakwidth <- min_peakwidth;
};
if (missing(max_peakwidth)){
peakParams$max_peakwidth <- 30;
} else{
peakParams$max_peakwidth <- max_peakwidth;
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh;
};
if (missing(noise)){
peakParams$noise <- 1000;
} else{
peakParams$noise <- noise
};
if (missing(prefilter)){
peakParams$prefilter <- 3;
} else{
peakParams$prefilter <- prefilter
};
if (missing(value_of_prefilter)){
peakParams$value_of_prefilter <- 100;
} else{
peakParams$value_of_prefilter <- value_of_prefilter
};
if (missing(criticalValue)){
peakParams$criticalValue <- 1.125;
} else{
peakParams$criticalValue <- criticalValue;
};
if (missing(consecMissedLimit)){
peakParams$consecMissedLimit <- 2;
} else{
peakParams$consecMissedLimit <- consecMissedLimit;
};
if (missing(unions)){
peakParams$unions <- 1;
} else{
peakParams$unions <- unions;
};
if (missing(checkBack)){
peakParams$checkBack <- 0;
} else{
peakParams$checkBack <- checkBack;
};
if (missing(withWave)){
peakParams$withWave <- FALSE;
} else{
peakParams$withWave <- withWave;
};
};
if (Peak_method=="matchedFilter"){
if (missing(fwhm)){
peakParams$fwhm <- 30;
} else{
peakParams$fwhm <- fwhm
};
if (missing(sigma)){
peakParams$sigma <- 12.74;
} else{
peakParams$sigma <- sigma
};
if (missing(steps)){
peakParams$steps <- 2;
} else{
peakParams$steps <- steps
};
if (missing(peakBinSize)){
peakParams$peakBinSize <- 0.1;
} else{
peakParams$peakBinSize <- peakBinSize
};
if (missing(max)){
peakParams$max <- 5;
} else{
peakParams$max <- max
};
if (missing(snthresh)){
peakParams$snthresh <- 10;
} else{
peakParams$snthresh <- snthresh
};
if (missing(mzdiff)){
peakParams$mzdiff <- 0.01;
} else{
peakParams$mzdiff <- mzdiff;
};
};
## Parameters for Grouping-Density Method Only
if (missing(bw)){
peakParams$bw <- 10;
} else{
peakParams$bw <- bw;
};
if (missing(minFraction)){
peakParams$minFraction <- 0.8;
} else{
peakParams$minFraction <- minFraction
};
if (missing(minSamples)){
peakParams$minSamples <- 1;
} else{
peakParams$minSamples <- minSamples
};
if (missing(maxFeatures)){
peakParams$maxFeatures <- 100;
} else{
peakParams$maxFeatures <- maxFeatures
};
if (missing(fitgauss)){
peakParams$fitgauss<-FALSE
} else {
peakParams$fitgauss<-fitgauss
};
# if (missing(verbose.columns)){
peakParams$verbose.columns <- FALSE;
# } else{
# peakParams$verbose.columns <- verbose.columns
# };
if (missing(mzCenterFun)){
peakParams$mzCenterFun<-"wMean"
} else {
peakParams$mzCenterFun<-mzCenterFun
};
if (missing(integrate)){
peakParams$integrate<-1
} else {
peakParams$integrate<-integrate
}
## Parameters for RT correction
if (RT_method=="loess" | RT_method=="null"){ peakParams$RT_method="loess";
if (missing(extra)){
peakParams$extra <- 1;
} else{
peakParams$extra <- extra
};
if (missing(span)){
peakParams$span <- 0.4;
} else{
peakParams$span <- span
};
if (missing(smooth)){
peakParams$smooth <- "loess";
} else{
peakParams$smooth <- smooth
};
if (missing(family)){
peakParams$family <- "gaussian";
} else{
peakParams$family <- family
};
}
if (RT_method=="obiwarp"){
if (missing(profStep)){
peakParams$profStep <- 1;
} else{
peakParams$profStep <- profStep
};
# Set profStep only here, profStep equals binsize
# other parameters use default
}
}
## Generic Params
# if (missing(verbose.columns)){
peakParams$verbose.columns <- FALSE;
# } else{
# peakParams$verbose.columns <- verbose.columns
# };
### Platform Selection--OTHERS-Annotation---
### Setup Peak Annotation Parameters
if("annotation" =="annotation"){
# TO DO: add more annotation in future
if (missing(polarity)){
peakParams$polarity <- "negative";
} else{
peakParams$polarity <- polarity;
}
if (missing(perc_fwhm)){
peakParams$perc_fwhm <- 0.6;
} else{
peakParams$perc_fwhm <- perc_fwhm;
}
if (missing(mz_abs_iso)){
peakParams$mz_abs_iso <- 0.005;
} else{
peakParams$mz_abs_iso <- mz_abs_iso;
}
if (missing(max_charge)){
peakParams$max_charge <- 2;
} else{
peakParams$max_charge <- max_charge;
}
if (missing(max_iso)){
peakParams$max_iso <- 2;
} else{
peakParams$max_iso <- max_iso;
}
if (missing(corr_eic_th)){
peakParams$corr_eic_th <- 0.85;
} else{
peakParams$corr_eic_th <- corr_eic_th;
}
if (missing(mz_abs_add)){
peakParams$mz_abs_add <- 0.001;
} else{
peakParams$mz_abs_add <- mz_abs_add;
}
if (missing(adducts)){
peakParams$adducts <- NULL;
} else{
peakParams$adducts <- adducts;
}
}
# Set potential Contaminats removal (rmConts) or not
if(missing(rmConts)){
peakParams$rmConts <- TRUE;
} else {
peakParams$rmConts <- as.logical(rmConts);
}
# Set potential Contaminats removal (rmConts) or not
if(missing(BlankSub)){
peakParams$BlankSub <- TRUE;
} else {
peakParams$BlankSub <- as.logical(BlankSub);
}
#Output a table for display
if(.on.public.web()){
if(file.exists("params.rda")){
file.rename("params.rda", "params_last.rda")
}
save(peakParams,file="params.rda");
write.table(unlist(peakParams),file="param_default.txt",row.names = TRUE,col.names = FALSE,quote = FALSE);
write.table("NOT Finished Yet!",file="param_optimized.txt",row.names = TRUE,col.names = FALSE,quote = FALSE);
}
#### Other Parameters
# None for now !
return(peakParams)
}
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