#Amino Acid Data aadat <- scan(file="aa01.txt", what="", sep=" ") aq <- paste(aadat, sep="", collapse="") aqcode <- list() for (i in 1:2000) aqcode[[i]] <- substring(aq,i,i) aqcode <- as.matrix(aqcode) aa01.input <- aatocat(aqcode) aatocat <- function(x) { n <- length(x) aacat <- matrix(nrow=n,ncol=19) for (i in 1:n) { if(x[i,1][[1]] == "A") aacat[i,]<- c(1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "C") aacat[i,]<- c(0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "D") aacat[i,]<- c(0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "E") aacat[i,]<- c(0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "F") aacat[i,]<- c(0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "G") aacat[i,]<- c(0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "H") aacat[i,]<- c(0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "I") aacat[i,]<- c(0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "K") aacat[i,]<- c(0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "L") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "M") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "N") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0) if(x[i,1][[1]] == "P") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0) if(x[i,1][[1]] == "Q") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0) if(x[i,1][[1]] == "R") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0) if(x[i,1][[1]] == "S") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0) if(x[i,1][[1]] == "T") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0) if(x[i,1][[1]] == "V") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0) if(x[i,1][[1]] == "W") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1) if(x[i,1][[1]] == "Y") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0) } aacat <- na.omit(aacat) return(aacat) } aatocatnum <- function(x) { n <- length(x) aacat <- matrix(nrow=n,ncol=19) for (i in 1:n) { if(x[i,1][[1]] == "1") aacat[i,]<- c(1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "2") aacat[i,]<- c(0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "3") aacat[i,]<- c(0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "4") aacat[i,]<- c(0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "5") aacat[i,]<- c(0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "6") aacat[i,]<- c(0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "7") aacat[i,]<- c(0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "8") aacat[i,]<- c(0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "9") aacat[i,]<- c(0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "10") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "11") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0) if(x[i,1][[1]] == "12") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0) if(x[i,1][[1]] == "13") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0) if(x[i,1][[1]] == "14") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0) if(x[i,1][[1]] == "15") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0) if(x[i,1][[1]] == "16") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0) if(x[i,1][[1]] == "17") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0) if(x[i,1][[1]] == "18") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0) if(x[i,1][[1]] == "19") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1) if(x[i,1][[1]] == "20") aacat[i,]<- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0) } aacat <- na.omit(aacat) return(aacat) }