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#' Generate values for metabolites normalization
#'
#' According to the area of QC along each day, this function generates values for each sample injected along the day that are going to be used for data normalization.
#' @param LCdata Matrix of data obtained (mainly by LC-MS) that included four data columns ("Compound Name","Order","QC","Day") and then one coulm for each compound or entity detected.
#' @examples
#' \dontrun{
#' correctedLCdata<-QCcorrectionLOESS(LCdata)
#' }
#' @export
#' @import plyr
#' @importFrom stats lm
#' @importFrom stats na.omit
#' @importFrom stats coefficients
#' @importFrom stats poly
#' @return A data set similar to LCdata matrix but with duplicated columns for each compound or entity with the area needed to normalize each of them.
QCcorrectionLOESS<-function(LCdata) {
globalenv()
LCdata<-LCdata
LCdataframe<-as.data.frame(LCdata)
LCdataQC<-subset(LCdata,LCdata$QC==1)
PreCompoundsList<-colnames(LCdata)
InfoColumns<-c("Sample","Order","QC","Day")
CompoundsList<-setdiff(PreCompoundsList,InfoColumns)
LCdatanew<-LCdata
m=1;
while(m<(length(CompoundsList)+1)){
lmloess<-loess(LCdata[,CompoundsList[m]]~(LCdata[,"Order"]),span=0.3,degree=2);
LCdatanew[,paste0(CompoundsList[m],'QC')]<-predict(lmloess,LCdata[,"Order"]);
m<-m+1
}
PreNormLCdata<-LCdatanew
p=1;
while(p<(length(CompoundsList)+1)){
PreNormLCdata[,paste0(CompoundsList[p],'_Norm')]<-PreNormLCdata[,(CompoundsList[p])]/PreNormLCdata[,paste0(CompoundsList[p],'QC')]
p<-p+1
}
NormLCdata1<-PreNormLCdata[,grepl("Norm",names(PreNormLCdata))]
NormLCdata2<-PreNormLCdata[,InfoColumns]
NormLCdata<-cbind(NormLCdata2,NormLCdata1)
return(NormLCdata)
}
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