Kurt -- If you create a vector of alignment positions, you should be able to do
alignment.pos <- rep(1:236, each = 72) table(data.frame(as.vector(align1), alignment.pos)) You may want to coerce align1 to a factor with appropriate levels, in case you are missing some amino acids. Otherwise there's an automatic coercion, I believe, and you will use only the levels actually present in your data. Here's an example using the first 10 letters of the alphabet instead of the amino acid set: > align1 <- matrix(sample(LETTERS[1:10], 200, replace = TRUE), nr = 5, nc = 40) > alignment.pos <- rep(1:40, each = 5) > table(data.frame(as.vector(align1), alignment.pos)) Hope this helps, Matt Wiener -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Wollenberg, Kurt R Sent: Thursday, January 06, 2005 11:36 AM To: 'r-help@stat.math.ethz.ch' Subject: [R] Calculating a table of symbol frequencies Hello all: I have a protein sequence alignment in a data frame (align1, 72 x 236), where each row is a protein and each column a site in the alignment. AA is vector of amino acid symbols plus "-" (gap). I can calculate amino acid frequencies at each site by: >align1.F <- matrix(0,nrow=22,ncol=236,dimnames=list(AA,seq(1:236))) >for(i in 1:236) > align1.F[names(summary(align1[[i]])),i] <- (summary(align1[[i]])/length(align1[[i]])) Is there a more efficient (i.e., without a loop) way to do this? Is there some way to use table or ftable to create an 22 x 236 table of amino acid frequencies from align1 and AA in one fell swoop? Thanks, Kurt Wollenberg, PhD Tufts Center for Vision Research New England Medical Center 750 Washington St, Box 450 Boston, MA, USA [EMAIL PROTECTED] 617-636-8945 (Fax) 617-636-9028 (Lab) The most exciting phrase to hear in science, the one that heralds new discoveries, is not "Eureka!" (I found it!) but "That's funny ..." --Isaac Asimov ********************** Confidentiality Notice\ **********************\ The inf...{{dropped}} ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
