similar to: Calculating symbol (letter) 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) >

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:

Hello all: I have written a few R scripts and am trying to turn them into a package for submission to CRAN. All of these scripts are R code only, no C or C++ or anything else. I'm working with R 2.0.1 running on a Windows XP machine. So far running ">rcmd install --build --docs=normal mypkge" seems to work (i.e., the library "mypkge" is installed in R\rw2001\library and

Dear R-helpers: thank your for your attention. i am a newer to R and i am doing some protein category classification based on the amino acid sequence.while i have some questions urgently. 1. any packages for analysis amino acid sequence 2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB" 3. based on "AAABBB",how can i get some

Dear all, I am a R beginner, and I am looking for a way to do the same thing for all levels of a column in a table. Basically, I have a bunch of protein sequences composed of different amino acid residues, and each residue is represented by an uppercase letter. I want to calculate the ratio of different amino acid residues at each position of the proteins. Here is an example table: Proteins

Dear R-helpers: thank your for your attention. i am a newer to R and i am doing some protein category classification based on the amino acid sequence.while i have some question urgent. 1. any packages for analysis amino acid sequence 2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB" 3. based on "AAABBB",how can i get some

hello every one, How to function more than one loop in R? I have the following problem to be solved with the a method of three loops, can you help me please? The data is attached with this message. The data is composed of two parts, cleaved (denoted by ?cleaved?) and non cleaved (denoted by ?noncleaved?). ? to access to the ith peptide, you can use X$Peptide[i] ? to access to the ith label,

hi i am new to R language. I want to use aaMI package which calculates the amino acid mutual interaction for a given protein sequence. I had installed the package but when i run the program it gives me the error could not find function "aaMI". can anyone tell me what might be the problem.. -- View this message in context: http://www.nabble.com/aaMI-tp14915744p14915744.html Sent from

library(sos) (mp <- findFn('{molecular properties}')) ????? ** found 7 matches in 4 packages and opened two web pages in my default browser with (a) the 7 matches and (b) the 4 packages. The first function was something for amino acids, like you suggested.? Two others returned compound and substance information from PubChem. ????? Does this help? ????? Spencer On

All Is there a package or library that will, given a nucleotide sequence 1. calculate the extinction coefficient at 260 nm for (Beer-Lambert's law) 2. calculate molecular weight 3. return it's complementary sequence I was able to find several packages that can do similar calculations for an amino acid sequence for proteins but none for nucleic acids. Any pointers, etc. would be

Dear mailing list, I'm stuck with a tricky problem here - at least it seems tricky to me, being not really talented in pattern matching and regex matters. I'm analysing amino acid mutations by position and type of mutation. E.g. (fictitious example) in position 92, I can find L92V, L92MV, L92I... L is in this example the wild-type amino-acid, and everything behind the position number is

I have following codes for ggplots. The legends are given in the plot do not match with the values specified in the codes given below. Your helps highly appreciated. Greg library(ggplot2) p <- ggplot(a,aes(x=NO_BMI_FI_beta ,y=FI_beta ,color= Super.Pathway))+ theme_bw() +theme(panel.border=element_blank()) + geom_point(size=3) p2<-p+scale_color_manual(name="Super.Pathway",

... In addition, you may wish to also post on the Bioconductor list for this sort of thing. -- Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Thu, May 3, 2018 at 12:58 AM, Spencer Graves <spencer.graves at effectivedefense.org>

Dear All, I would like to generate random protein sequences using a HMM model. Has anybody done that before, or would you have any idea which package is likely to be best for that? The important facts are that the HMM will be fitted on ~3 million sequential observations, with 20 different states (one for each amino acid). I guess that 2-5 hidden states should be enough, and an order of 3 would

Dear all, I am trying to make a series of waffle plot-like figures for my data to visualize the ratios of amino acid residues at each position. For each one of 37 positions, there may be one to four different amino acid residues. So the data consist of the positions, what residues are there, and the ratios of residues. The ratios of residues at a position add up to 100, or close to 100 (more on

Greetings: In a function I'm trying to write I am multiplying each row in a matrix by a vector. When the vector extends beyond the end of the matrix I need to have the multiplication wrap around (continue with column 1 of the matrix). Initially I got this to work with a loop (old programming habits die hard). Now, after going back through MASS I've figured out how to do the multiplication

Greetings all: OK, this is bugging the @#@%* out of me. I know the answer is simple and straightforward but for the life of me I cannot find it in the documentation, in the archives, or in my notes (because I know I've encountered this in the past). My problem is: I have a data frame with columns A, B, C, D, and E. A, B, and E are factors and C and D are numeric. I need a new data frame with

Hi there, I have a large amino acid csv file like this: input.txt: P,LV,Q,Z P,VL,Q,Z P,ML,QL,Z There is a problem with this file, since LV and VL are in fact the same thing. How do I order each element according to alphabetical order so that the desired output would look like: output.txt: P,LV,Q,Z P,LV,Q,Z P,LM,LQ,Z -- View this message in context:

Dear R users, A new package, CHNOSZ (version 0.8), is available on CRAN. CHNOSZ is a package for thermodynamic calculations and analysis. Functions are available for calculating the standard Gibbs energies and other thermodynamic properties, and chemical affinities, of reactions between species contained in the thermodynamic database. The database includes standard thermodynamic properties

Dear R users, A new package, CHNOSZ (version 0.8), is available on CRAN. CHNOSZ is a package for thermodynamic calculations and analysis. Functions are available for calculating the standard Gibbs energies and other thermodynamic properties, and chemical affinities, of reactions between species contained in the thermodynamic database. The database includes standard thermodynamic properties