[R] caculate the frequencies of the Amino Acids

[David Winsemius]

On Jan 2, 2010, at 12:26 AM, David Winsemius wrote:

>
> 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)

Further thoughts: If I understand how you are doing this, that  
structure would only be large enough for one string's results.

(Seems like this process would be easier if you used table() instead  
of for-loops.)

>> 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
>> -- 
>> View this message in context: http://n4.nabble.com/caculate-the-frequencies-of-the-Amino-Acids-tp997072p997072.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
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>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.