[R] caculate the frequencies of the Amino Acids

[che]

Thanks very much the code is working perfectly, but I hope guys that you can
help me to do the same thing but by using the loop structure, i want to know
if i am doing right, i want to use the loop structure to scan each sequence
from the file sequence.txt (the file is attached) to get the frequency for
each Amino Acid, and i wrote the following code so far, and i stopped, got
confused, specially that i am a very beginner in R
http://n4.nabble.com/file/n997581/sequence.txt sequence.txt :
x<-read.table("sequence.txt",header=FALSE)
AA<-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')

test<-nchar(as.character(x$V1[i]))
frequency<-function(X)
{
y<-rep(0,20)
for(j in 1:test){
for(i in 1:nrow(x)){
	res<-which(AA==substr(x$V1[i],j,j))
	y[res]=y[res]+1
	}
	}
return(y)
}
So how to fix this code, how to give the life for the “i” and the “j” in
order to initiate the indexing..... Sorry for bothering you guys.


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 
> 

-- 
View this message in context: http://n4.nabble.com/caculate-the-frequencies-of-the-Amino-Acids-tp997072p997581.html
Sent from the R help mailing list archive at Nabble.com.