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COMPOSITION.R
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COMPOSITION.R
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##encoding methods
NC1 <- function(data){
for(i in 1:length(data) ){
if(i==1){
DCfirst <- unlist(as.vector(strsplit(data[1],"",fixed = TRUE)))
DCsecond <- matrix(NA,nrow = length(data),ncol = length(DCfirst))
DCsecond[1,] <- DCfirst
}else{
DCsecond[i,] <- unlist(as.vector(strsplit(data[i],"",fixed = TRUE)))
}
}
return(DCsecond)
}
library(matrixStats)
CONPOSITION <- function(Data,NI=3,NTYPE="RNA",Freq=2){
# MA <- NC1(DATA)
if(NTYPE=="RNA"){
U="U"
}else{
U="T"
}
for(i in 1:NI){
if(i==1){
NP <- c("A","G","C",U)
}else{
NP1 <- NULL
for(j in c("A","G","C",U)){
for(k in 1:length(NP)){
NP1 <- c(NP1,paste0(NP[k],j))
}
}
NP <- NP1
}
}
MA2 <- matrix(NA,ncol = length(NP),nrow = length(Data))
colnames(MA2) <- NP
if(NTYPE=="RNA"){
for(i in 1:length(NP)){
MA2[,i]<- vcountPattern(NP[i],RNAStringSet(Data))
}
}else{
for(i in 1:length(NP)){
MA2[,i]<- vcountPattern(NP[i],DNAStringSet(Data))
}
}
M3 <- MA2
if(Freq==1){
for(i in 1:nrow(M3)){
M3[i,] <- MA2[i,]/sum(MA2[i,])
}
}
return(M3)
}