caculate the frequencies of the Amino Acids
i know it would be better to ask R to make the data, but i need to sequence this particular file, because it is data for some Amino Acids and i cant play with, so i need to ask R to go through the sequence one by one, and then give me the numbers of each letters of each sequence, i am quite confused between using "i" and "j" and how to iterate both of them and make them work functionally. i attached the sequence.txt with my original message, and i will attach it here in case. thanks for your help. http://n4.nabble.com/file/n997087/sequence.txt sequence.txt
che wrote:
may some one please help me to sort this out, i am trying to writ a R code
for calculating the frequencies of the amino acids in 9 different
sequences, i want the code to read the sequence from external text file, i
used the following code to do so:
x<-read.table("sequence.txt",header=FALSE)
then i defined an array for 20 amino acids as following:
AA<-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
i am using the following code to calculate the frequencies:
frequency<-function(X)
{
y<-rep(0,20)
for(j in 1:nchar(as.character(x$V1[i]))){
for(i in 1:9){
res<-which(AA==substr(x$V1[i],j,j))
y[res]=y[res]+1
}
}
return(y)
}
but this code actually is not working, it reads only one sequence, i dont
know why the loop is not working for the "i", which suppose to read the
nine rows of the file sequence.txt. the sequence.txt file is attached to
this message.
cheers
http://n4.nabble.com/file/n997072/sequence.txt sequence.txt
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