Nothing
freqCompute=function(mat=mat,refseq=refseq){
freqR=list()
refaa=translate_cm(s2c(refseq))
allmutations=list()
newMat=c()
patternLabel=c()
for(i in 1:dim(mat)[1]){
specific_row=mat[i,]
amino_set=setdiff(unique(specific_row[specific_row!=refaa[i]]),c("X","*"))
for(am in amino_set){
NY=sum(specific_row==am)
newMat=rbind(newMat,as.numeric(specific_row==am))
targetbp=s2c(refseq)[((i-1)*3+1):(i*3)]
names_label=paste(translate_cm(targetbp),am,sep=as.character(i))
patternLabel=append(patternLabel,names_label)
freqd=round(NY/dim(mat)[2],digits=3)
#names(freqd)=names_label
allmutations[[names_label]]=freqd
}
}
rownames(newMat)=patternLabel
freqR$newMat=newMat
freqR$allmutations=allmutations
return(freqR)
}
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