caculate the frequencies of the Amino Acids
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
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