similar to: dna library

Hi, I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, Heterozygosity and such summary statistics. Package Adagenet converts the DNA sequence into retaining only retaining the polymorphic sites and then calcuates Fst.. but is there any other way to do this? I mean analyse the DNA sequence as it is.. and calculate the statistics? Thanks! [[alternative HTML version deleted]]

Hello - I cannot get to www.alpha.luc.ac.be/~jlindsey/rcode.html<http://www.alpha.luc.ac.be/%7Ejlindsey/rcode.html>to obtain and install the repeated library for use of glmm(). Is the web page not active? Can you give me an alternative location to obtain the repeated library? Thank you, Becky Parker [[alternative HTML version deleted]]

Hi all, Does anyone know what happened to the dna library or the dotmatrix function? For the life of me, I can't find it anywhere with the exception of this reference: http://rss.acs.unt.edu/Rdoc/library/dna/html/dotmatrix.html Thanks! Jeff. http://www.nd.edu/~jspies/ [[alternative HTML version deleted]]

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Hi all, I am learning R by "doing". And this is my first post. I want to use R: 1- to fetch a DNA sequence from a databank (see bellow) and 2- store it as FASTA file. The problem: neither an error is prompted nor the fasta file is created. Testing the code (see bellow), I notice that everything works until the *"write.dna" *command - which is not creating the fasta file.

Hi, I am making some DNA distances and I would like to use dist.dna as matrix in R, but this command does not include models like GTR... Is there some command or alternative using dist.dna in ape package for models not included like GTR? I would appreciate any help given Thank you very much, Ignacio Quintero Laboratorio de biología evolutiva de vertebrados (Evolvert) Departamento de Ciencias

I suspect you meant WD <- "~/Documents/Scripting/R_Studio/Sequences/" but I am entirely unfamiliar with the packages you are using, and know nothing about what is on your hard drive. For future reference: A) Read the Posting Guide. This is a plain text email list, and your html formatting gets removed leaving a mess that is not always readable. B) Most frequent users of R

I have just put the postscript file for the first draft of a manuscript of a course on The Statistical Analysis of Stochastic Processes in Time, as well as the R code to do all of the examples, on my web page at www.luc.ac.be/~jlindsey/manuscripts.html The chapters are Part I Basic principles 1. What is a stochastic process? 2. Normal theory models and extensions. Part II Categorical state

I have just put the postscript file for the first draft of a manuscript of a course on The Statistical Analysis of Stochastic Processes in Time, as well as the R code to do all of the examples, on my web page at www.luc.ac.be/~jlindsey/manuscripts.html The chapters are Part I Basic principles 1. What is a stochastic process? 2. Normal theory models and extensions. Part II Categorical state

Dear all, I was wondering how to read DNA sequences in R, is there a specific function and/or a specific package for that? Thank you very much in advance, Gian ** [[alternative HTML version deleted]]

>>>>> "Jim" == Jim Lindsey <jlindsey@alpha.luc.ac.be> writes in a private mail to me Jim> That bug in seq() really has shaken my faith in R. How Jim> many other known bugs are there that we on r-help are not informed Jim> of and which can falsify our statistical analyses??? It is Jim> imperative that patches for such things be made

================================================= This is an automated summary of the status of the R-bugs repository. Note that this may be neither complete nor perfectly correct at any given instance: Not all bugs are reported, and some reported bugs may have been fixed, but the repository not yet updated. Some bug fixes are difficult to verify because they pertain to specific hardware or

I was wondering if anyone out there has created a series of images (e.g. jpegs) using R, then animated them on a web page. I have looked around a bit and it seems fairly complicated. One approach that seems sensible is to use a java script that displays the list of images. I have only used html on web pages before so I don't know how to use java... Ideally the final result is easily ported to

Hello, I have a question about margins when plotting an unrooted tree (type="unrooted") with the 'ape' package ver. 1.7. When I plot an unrooted tree with: no.margin=TRUE it seems that the margins are still there. It appears to be only when type="unrooted". I'm plotting multiple plots using layout() and would like to be able to get rid of the margins or if

An executable version 0.6 of my libraries is now available at www.luc.ac.be/~jlindsey/rcode.html This works with MS R0.64.2 and appears possibly to work with R65.0. There is a serious problem with the Fortran compiler as some of the examples for elliptic and carma crash it. These same examples do not crash R63.0 with the library executables of Jan 99. I am releasing this anyway because of the

================================================= This is an automated summary of the status of the R-bugs repository. Note that this may be neither complete nor perfectly correct at any given instance: Not all bugs are reported, and some reported bugs may have been fixed, but the repository not yet updated. Some bug fixes are difficult to verify because they pertain to specific hardware or

I have been implementing a proposal of Jim Lindsey for glm(.) to return AIC values, and print.glm(.) and print.summary.glm(.) printing them.... however: >>>>> "Jim" == Jim Lindsey <jlindsey@luc.ac.be> writes: Jim> The problem still remains of getting the correct AIC when the user Jim> wants the scale parameter to be fixed. (The calculation should

================================================= This is an automated summary of the status of the R-bugs repository. Note that this may be neither complete nor perfectly correct at any given instance: Not all bugs are reported, and some reported bugs may have been fixed, but the repository not yet updated. Some bug fixes are difficult to verify because they pertain to specific hardware or

There are some tools for handling genetic data in the 'genetics' package on CRAN. These were motiviated by the need to process population genetic data. -G > -----Original Message----- > From: Daniel Edmund Davison [mailto:davison at midway.uchicago.edu] > Sent: Monday, May 05, 2003 1:58 PM > To: r-help at stat.math.ethz.ch > Subject: [R] DNA > > > > Hi, is

Prof. Javier Cabrera will be giving the online course "DNA Microarray Data Analysis" from Jan. 28 - Feb. 25 at statistics.com. Dr. Cabrera is co-author of "Exploration and Analysis of DNA Microarray and Protein Array Data" (the course text; Wiley) and has published a number of articles on gene expression data analysis, data mining and multivariate methods in leading