Hi fadialnaji,

Take a look at the Biostring package in Bioconductor [1] It might be an
alternative to do what you want.

HTH,
Jorge

[1] http://www.bioconductor.org/packages/release/bioc/html/Biostrings.html


On Fri, 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$V1[i]))){
> for(i in 1:9){
>
>        res<-which(AA==substr(x$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-tp997072p997072.html
> Sent from the R help mailing list archive at Nabble.com.
>
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