[R] caculate the frequencies of the Amino Acids

[che]

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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