I sent a private reply to the poster yesterday with the solution to his
problem,
bit evidently he hasn't seen it, so ...
# Function to tabulate an amino acid sequence
# using strsplit and table:
AAtab2 <- function(x) {
# Creates a frequency table of the characters in a string
AA <- LETTERS[-c(2, 10, 15, 21, 24, 26)]
n <- nchar(x)
s <- substring(x, 1:n, 1:n)
table(factor(s, levels = AA))
}
AAtabMatrix <- function(x) {
# Input x is an amino acid sequence as a character string
if(!is.character(x)) stop('Input must be a character string or vector.')
do.call(rbind, lapply(as.list(x), AAtab2))
}
cheseq <- scan(url('http://n4.nabble.com/file/n997581/sequence.txt'), what =
'')
> AAtabMatrix(cheseq)
A C D E F G H I K L M N P Q R S T V W Y
[1,] 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[2,] 21 0 25 28 27 24 0 34 39 31 11 20 16 10 17 25 22 33 3 15
[3,] 34 5 15 25 6 35 7 24 23 32 9 12 15 10 17 14 13 36 2 13
[4,] 33 5 17 24 7 36 7 24 24 32 9 13 14 9 17 12 14 36 2 12
[5,] 33 5 16 25 5 35 6 24 23 33 8 12 15 9 17 17 12 35 2 15
[6,] 33 4 15 6 21 30 3 19 23 22 8 8 8 14 17 14 12 24 5 12
[7,] 30 3 13 4 16 22 2 17 16 17 6 6 7 11 15 11 12 18 3 11
[8,] 39 5 21 8 22 39 2 23 29 25 10 8 7 13 22 14 21 25 7 16
[9,] 34 4 17 6 19 30 2 20 24 21 8 7 7 12 17 14 16 21 5 14
[10,] 35 4 17 6 18 31 3 20 23 21 8 7 7 12 18 12 17 21 5 13
Each row represents the frequency table of an individual AA sequence.
DM
On Sat, Jan 2, 2010 at 9:28 PM, che <fadialn...@live.com> wrote:
>
> 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.
>
> ______________________________________________
> R-help@r-project.org mailing list
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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