Nothing
aaVLFs.to.modalchanges <-
function(modal, AminoAcidList, aalength){
polarcharged <- c("D", "E", "K", "R", "H")
polaruncharged <- c("S", "T", "Q", "N", "Y")
Nonpolar <- c("A", "V", "L", "I", "M", "F", "W")
Unique <- c("G", "C", "P")
positionAllAminos <- list()
p <- 1
for(i in 1:nrow(AminoAcidList)){
for(n in 1:aalength){
if(is.na(AminoAcidList[i, n+2]) == FALSE){
positionAllAminos[[p]] <- c(AminoAcidList[i,1], AminoAcidList[i, 2], n, AminoAcidList[i,n+2])
p = p + 1
}
}
}
sameAll <- 0
changedAll <- 0
z <- c()
r <- c()
for(i in 1:length(positionAllAminos)){
z[i] <- (modal[as.numeric(positionAllAminos[[i]][3])])
r[i] <- positionAllAminos[[i]][4]
if(any(z[i] == polaruncharged) && any(r[i] == polaruncharged)){
sameAll = sameAll + 1
}else{
if(any(z[i] == polarcharged) && any(r[i] == polarcharged)){
sameAll = sameAll + 1
}else{
if(any(z[i] == Nonpolar) && any(r[i] == Nonpolar)){
sameAll = sameAll + 1
}else{
if(any(z[i] == Unique) && any(r[i] == Unique)){
sameAll = sameAll + 1
}else{changedAll = changedAll + 1}
}
}
}
}
return(rbind(sameAll,changedAll))
}
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