[R] caculate the frequencies of the Amino Acids

[David Winsemius]

On Jan 1, 2010, at 11:59 PM, 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$V1[i]))){
# at this point you are referencing "i" but it is not yet being  
iterated and might not even exist.
# did you mean "j"?
# also might be  safer to use seq_along()
> for(i in 1:9){
>
> 	res<-which(AA==substr(x$V1[i],j,j))

# Is that really working for even one sequence? Without an "x"  
sequence I cannot test, but it "looks wrong".

> 	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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>
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