similar to: ape 0.1 is released

Dear R-users, Thanks to Friedrich Leisch, my document "R pour les d?butants" is available on CRAN in the contributed documentation section: http://cran.r-project.org/doc/contrib/Rdebuts.pdf. It is written in French. "R pour les d?butants" ("R for beginners") gives a starting point for people with no experience with R (or S). I tried to explain the basics in the

Dear R-users, Thanks to Friedrich Leisch, my document "R pour les d?butants" is available on CRAN in the contributed documentation section: http://cran.r-project.org/doc/contrib/Rdebuts.pdf. It is written in French. "R pour les d?butants" ("R for beginners") gives a starting point for people with no experience with R (or S). I tried to explain the basics in the

Dear all, The version 1.0 of ape (analysis of phylogenetics and evolution) is now on CRAN. The jump from version 0.2-1 to 1.0 is explained by the fact that the initial objectives of the project have been completed. The relevant part of the Changes file is shown below. All comments, suggestions, or bug reports are welcome. Emmanuel Paradis CHANGES IN APE VERSION 1.0 NEW FEATURES

Dear All, I have two distributions which I don't their nature. I want to check whether they come from the same distribution. I know that I can use KS test however the standart function ks.test applies only the ks test for testing the difference of two samples (non-parametric). By the way the distribution are of Euclidean distances. One of observed and the other of shuffled data. Thanks, Ron

Hi, If I have a CSV file which has several comments at the top, and the data start immediately after the line: @DATA Is it possible to use the scan() command to get the CSV data into R, by only reading the lines after @DATA? If so, how can I do it? Cheers, Kevin ------------------------------------------------------------------------------ /* Time is the greatest teacher, unfortunately it

Dear all: I have a character object x with ' (single-quote) character. x <- c('"hydrolase activity","actin binding","3',5'-cyclic-nucleotide phosphodiesterase activity") I want to write a function that will identify ' and replaces with \' myf <- function(term){ if (grep("'",term)) {

Hello, I'm struggling with understanding the output on the ancestral.pars() command from the phangorn package, I'm new to doing phylogenetic analyses using R. I used it on nucleotide data, and it works fine, I'm just not sure how to read the output. The output is phyDat class, and outputs a matrix for each node/leaf in the tree. I figured out that the matrix columns represent the four

At 11:57 25/10/00 +0100, Brian Ripley wrote: >> Date: mer., 25 oct. 2000 12:38:55 +0200 >> From: Emmanuel Paradis <paradis@isem.univ-montp2.fr> > >> I think it would be nice to have par(ask=T) set by default in termplot(), >> like it is in plot.lm(). > >Well, it isn't really the default in plot.lm, the default for `ask' being > >interactive()

Dear useRs, The seqinR package is a library of utilities to retrieve and analyse biological sequences. A new version of seqinR, seqinR 1.0-7, has been released on CRAN. Here is a summary of changes: o A new *experimental* function extractseqs() to download sequences thru zlib compressed sockets from an ACNUC server is released. Preliminary tests suggest that working with about 100,000

Dear useRs, The seqinR package is a library of utilities to retrieve and analyse biological sequences. A new version of seqinR, seqinR 1.0-7, has been released on CRAN. Here is a summary of changes: o A new *experimental* function extractseqs() to download sequences thru zlib compressed sockets from an ACNUC server is released. Preliminary tests suggest that working with about 100,000

The new package RFLPtools is available on CRAN. RFLPtools provides analysis functions for DNA fragment molecular weights (e.g.\ derived from RFLP-analysis) and nucleotide sequence similarities. It aims mainly at the identification of similar or identical fragment patterns to evaluate the amount of different genotypes gained from environmental samples during diversity studies and at further

The new package RFLPtools is available on CRAN. RFLPtools provides analysis functions for DNA fragment molecular weights (e.g.\ derived from RFLP-analysis) and nucleotide sequence similarities. It aims mainly at the identification of similar or identical fragment patterns to evaluate the amount of different genotypes gained from environmental samples during diversity studies and at further

There seems to be a bug with var() when the argument is a vector with exactly three values of 1e30 (or close to this value). This does not happen with twice, four (or more) times this value, or another value. > var(rep(1e30, 3)) [1] 2.971056e+28 > var(rep(1.2e30, 3)) [1] 2.971056e+28 > var(rep(0.9e30, 3)) [1] 2.971056e+28 > var(rep(0.8e30, 3)) [1] 0 > var(rep(1e29, 3)) [1] 0 >

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",

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

Hi, I've been investigating the ape package for a while, and I was wondering if it is possible to: - display the names of the internal nodes (from a newick tree) - plot a pie-chart on top of each of the internal branches in a phylogram plot Thanks in advance, Cheers, Albert.

Hi there, I am looking for R-packages that can help me visualize properties on nucleotide sequences. I want to display sequences in the 1-100K base range as lines and plot features above and below those lines. Any ideas would be welcome. Thanks, Bernd

Hi, I am very new to R and wanted to know if there is a package that, given very long nucleotide sequences, searches and identifies short (7-10nt) motifs.. I would like to look for enrichment of certain motifs in genomic sequences. I tried using MEME (not an R package, I know), but the online version only allows sequences up to MAX 60000 nucleotides, and that's too short for my needs..

Hi there, I am looking for R-packages that can help me visualize properties on nucleotide sequences. I want to display sequences in the 1-100K base range as lines and plot features above and below those lines. Any ideas would be welcome. Thanks, Bernd [[alternative HTML version deleted]]

I think you mean between column 1 and 2 of A? Why is 36003918 not included? It is clearly between 35838396 and 36151202 in the first row of A. My earlier solution should work fine. Just create a new matrix AX that has the columns switched so that the start is always column 1 and use that to identify the ones you want to select. That way you are not modifying B. This will be faster than checking