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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