similar to: seqinr-dist.alignment?

Dear R users, seqinR 1.0-5 has been released yesterday on CRAN, so that the source code of the package should be available on all CRAN mirrors within the next 24h. The updated package vignette is here: http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-5.pdf User level visible changes are: o A new function dotPlot() is now available.

Dear R users, seqinR 1.0-5 has been released yesterday on CRAN, so that the source code of the package should be available on all CRAN mirrors within the next 24h. The updated package vignette is here: http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-5.pdf User level visible changes are: o A new function dotPlot() is now available.

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusion list: http://pbil.univ-lyon1.fr/software/SeqinR//mailing.php?lang=eng A

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusion list: http://pbil.univ-lyon1.fr/software/SeqinR//mailing.php?lang=eng A

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

Hi !  Facing problem with " getSequence" commend .  when only biomaRt package loaded the following example working well  >mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) show(seq) but when i have loaded the seqinr, i got problem

Good afternoon. I am a master student in University of Porto in Portugal. At this moment I’m starting to use R, so I have some doubts. The aim of my analysis is: calculate a pairwise FST matrix from fasta file and creat a principal component analyses with adegenet package (I use seqinr and ape package to read this file, then I convert this file into a genind object with DNA2genind function

Dear R developers, I am visualising high dimensional genomic data and for this purpose I need to compute pairwise distances between many points in a high-dimensional space (say I have a matrix of 5,000 rows and 20,000 columns, so the result is a 5,000x5,000 matrix or it's upper diagonal).Computing such thing in R takes many hours (I am doing this on a Linux server with more than 100 GB of RAM,

Hello, I am working with a matrix of multilocus genotypes for ~180 individual snail samples, with substantial missing data. I am trying to calculate the pairwise genetic distance between individuals using the stats package 'dist' function, using euclidean distance. I took a subset of this dataset (3 samples x 3 loci) to test how euclidean distance is calculated: 3x3 subset used

So I have a text file that looks like this: "Label" "X" "Y" "Slice" 1 "Field_1_R3D_D3D_PRJ_w617.tif" 348 506 1 2 "Field_1_R3D_D3D_PRJ_w617.tif" 359 505 1 3 "Field_1_R3D_D3D_PRJ_w617.tif" 356 524 1 4 "Field_1_R3D_D3D_PRJ_w617.tif" 2 0 1 5 "Field_1_R3D_D3D_PRJ_w617.tif" 412 872 1 6

Hi Everyone, I am a graduate student who will be using R to do my analysis. I need to do a spatial analysis, and the first step is to calculate the geographic distance between my study sites. I am hoping to use earth.dist because it allows for multiple pairwise distances to be calculated at one time. I have done a sample calculation, and I seem to have a problem between the steps of using

Hi, For the last few days I have tried utilise your package "pegas" in order to obtain some values for indices like the nuclear diversity and tajimas d value. I have modified my dataset (a text file containing dna sequences) in order to be able to read it in with the tools provided by pegas. Here, I have oriented myself on the description provided by the help-page in read.loci().

Hi Stefan, Thank you very much for pointing me to the wordspace package. It does the job a bit faster than my C code but is 100 times more convenient. By the way, since the tcrossprod function in the Matrix package is so fast, the Euclidean distance can be computed very fast: euc_dist <- function(m) {mtm <- Matrix::tcrossprod(m); sq <- rowSums(m*m);? sqrt(outer(sq,sq,"+") -

Hi I would like to use 'write.fasta(sequences, names, nbchar = 60, file.out, open = "w")' to convert a DNA sequence in a text file to fasta format. How do I read the the text file to prepare the argument 'sequences' of the function. The DNA sequence in the text file is one line as below: ATCACACAACGACACTCACCCTGGACGCTCATC......... Thank you [[alternative HTML

R-List, I'm trying to compute pairwise distances among pairs of observations, which each pair containing data from 2 groups. There are more than 100000 unique pairs. I have programmed a distance function that has three parameters, a vector of covariates from the ith observation in Group 1, a vector of covarites from the jth observation in Group 2, and a weighting matrix. I have used

Hi, I have just encountered a strange behaviour from 'cor' with regards to the treatment of NAs when calculating Spearman correlations. I guess it is a subtle bug. If I understand the help page correctly, the two modes 'complete.obs' and 'pairwise.complete.obs' specify how to deal with correlation coefficients when calculating a correlation _matrix_. When calculating

Odd behaviour of function cor() in R-2.10.1-64bit-Unix In a dataset with 1366 patients and 244 clinical variables Spearman's Rho was calculated for some fatty acids and BMI and came over something rather odd: R seems to calculate Rho differently on 2.10.1-64bit-Unix and 2.9.0-32bit-Windows when I calculate the complete (244x244) correlation matrix and then pick out the values I am

Dear R developers I am currently working on the seqinR package. The seqinR package allows a remote access to biological databases via a socket connection. We are using the functions socketConnection, writeLines and readLines to open the socket, send request to the server and receive response from the server respectively. Recently, a new function implemented in the socket server allows

Dear useRs, we are organizing the following session Topic: Innovative Tools in Data Analysis Organizers: Achim Zeileis and Bettina Gruen at the First Workshop of the ERCIM Working Group on Computing & Statistics June 19-21, 2008 Neuchatel, Switzerland URL: http://www.dcs.bbk.ac.uk/ercim08 To improve the quality of statistical data analysis the provision of innovative tools which make new