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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