Nothing
#########################################QCKd (Quality control and Kd)#######################################################
##################################################HitSel################################################
hitSel <- function(File,AvgSet,CutOff,Kd = FALSE)
{
if(Kd == TRUE){
Norm <- File[File[,1] == CutOff,]
Final <- File[File[,AvgSet] < (0.2*Norm[,AvgSet]) & File[,AvgSet] != 0,]
return(Final)
}
Norm <- File[File[,1] == CutOff,]
Final <- File[File[,min(AvgSet)] > (5*mean(Norm[,min(AvgSet)])),]
for (i in min(AvgSet):max(AvgSet))
{
Selection <- File[File[,i] > (5*mean(Norm[,i])),]
Combined <- rbind(Selection,Final)
Final <- Combined[duplicated(Combined),]
}
return(Final)
}
#####################################################QC###############################################
QCon <- function(File1,ColSet)
{
Sig <- File1[,min(ColSet)] ##Column Calls
Sig2 <- File1[,max(ColSet)]
FVari1 <- File1[Sig/Sig2 > 0.5 & Sig/Sig2 < 2.0,]
FVari1 <- na.omit(FVari1)
return(FVari1)
}
##########################################################QCKd########################################
QCKd<-function(File1,File2 = NULL,Kd = FALSE,QC = TRUE,ColSet1 = NULL,ColSet2 = NULL,ColSet3 = NULL)
{
if (Kd == TRUE)
{
Kds <- File1[abs(log10(File1[,4])-log10(File2[,4])) > 1,]
File1 <- Kds
}
if (QC == TRUE){
QCon <- function(File1,ColSet){
Sig <- File1[,min(ColSet)] ##Column Calls
Sig2 <- File1[,max(ColSet)]
FVari1 <- File1[Sig/Sig2 > 0.5 & Sig/Sig2 < 2.0,]
FVari1 <- na.omit(FVari1)
return(FVari1)
}
if(is.null(ColSet2) == TRUE & is.null(ColSet3) == TRUE){
CSet1 <- QCon(File1,ColSet1)
return(CSet1)
} else if(is.null(ColSet3) == TRUE){
CSet1 <- QCon(File1,ColSet1)
CSet2 <- QCon(File1,ColSet2)
CSet <- rbind(CSet1,CSet2)
CSet <- CSet[duplicated(CSet),]
return(CSet)
} else{
CSet1 <- QCon(File1,ColSet1)
CSet2 <- QCon(File1,ColSet2)
CSet3 <- QCon(File1,ColSet2)
CSet <- rbind(CSet1,CSet2)
CSet <- CSet[duplicated(CSet),]
CSet <- rbind(CSet,CSet3)
CSet <- CSet[duplicated(CSet),]
return(CSet)
}
} else{
return(File1)
}
}
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