caculate the frequencies of the Amino Acids

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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