similar to: How learn a probabilities matrix from a large fasta file in R?

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

Hi all, I have a sequence file (fasta format) and want to calculate the rho statistics for dinucleotide abundance value on my data.. the code which I use is (using seqinr library and current working directory) seq_info<-read.fasta("gene.txt") rho(seq_info[1],2) but it yields only the dinucleotides, not their rho values, i.e, > rho(seq_info[1],2) aa ac ag at ca cc cg ct ga gc

I am trying to pull a subset form a large group of FASTA sequences. I need to pull them based on the annot and write.fasta them. I have my subset annot titles in a .csv. What is the way to go about this? I tried pulling the sequences from a .csv but then MEGA 5 was not happy when i tried to put them back and I need to use MEGA to keep my data uniform. Any help would be greatly appreciated Thank

Hi everybody, Maybe this question is quite simple but i just don't know how to make it. I have a matrix a somewhat like this one but bigger: > a f g h i j k a NA NA 11 16 21 26 b NA NA 12 17 22 27 c NA 8 13 18 23 28 d NA 9 14 19 24 29 e NA 10 15 20 25 30 And i want to get the rows which at most have 2 Na. Thanks in advance. Shi Jiantao [[alternative HTML version deleted]]

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

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 trying to analyse my data using amova (http://www.oga-lab.net/RGM2/func.php?rd_id=pegas:amova): My input to R is a DNA sequence file, format=fasta dna<- read.dna("XX.fasta", format="fasta") #left other options as default d<- dist.dna(dna, model="raw") g<- read.table("XXX.design") Load necessary libraries: library(pegas)

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.

Hi, i want to plot figure like this, http://www.cis.hut.fi/projects/somtoolbox/download/pics2/shotvs2_colorcode.png So is there a function or package in R can help me to do this. Any suggestion will be appreciated. Thanks in advance Jiantao Shi [[alternative HTML version deleted]]

https://bugzilla.samba.org/show_bug.cgi?id=5963 Summary: rsync fails with errors that make no sense... Product: rsync Version: 3.0.4 Platform: x86 OS/Version: Linux Status: NEW Severity: major Priority: P3 Component: core AssignedTo: wayned@samba.org ReportedBy: crhea@mayo.edu

Dear all, I have DNA sequence data which are fasta-formatted as >gene A;..... AAAAACCCC TTTTTGGGG CCCTTTTTT >gene B;.... CCCCCAAAA GGGGGTTTT I want to load only the lines that start with ">" where the annotation information for the gene is contained. In principle, I can remove the sequences before loading or after loading all the lines. I just wonder if there's a way to

Hi all, I know pnorm() is able to calculate a sequence of probabilities by providing a vector of means, and a single number for location and standard deviation. For example, pnorm(0.5,c(0.5,2),1) will produce [1] 0.5000000 0.0668072. However, I wonder if its multivariate counterpart mvtnorm can do the same thing? Namely, if I provide a sequence of (vector-)means and a single vector for

Hi - When I'm trying to read in a text file into a labeled character array, the memory stamp/footprint of R will exceed 4 gigs or more. I've seen this behavior on Mac OS X, Linux for AMD_64 and X86_64., and the R versions are 2.4, 2.4 and 2.2, respectively. So, it would seem that this is platform and R version independant. The file that I'm reading contains the upstream regions

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

Hi, I think I have configured everything correctly but for some reason I can?t get a list of the shared mailboxes to show up. When I run: doveadm acl debug -u m.markov Shared/d.marteva/INBOX doveadm(root): Debug: Skipping module doveadm_fts_plugin, because dlopen() failed: /usr/lib/dovecot/modules/doveadm/lib20_doveadm_fts_plugin.so: undefined symbol: fts_backend_rescan (this is usually

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 List, I have a couple of (~200) 3x3 transition probability matrices (ie each defines a Markov chain). They are all estimated from the same underlying process, so it ie meaningful to take their elemetwise mean and standard deviation. [1] First question: supposing that they are given in a list l, how do I get their elementwise mean and standard deviation? Fortunately, the mean of trans. prob.

Trixbox 2.2 Beta with freePBX 2.2.0rc1 I have a setup that looks something like this in ASCII art: Teliax IAX Trunk ------+ | V Embarq PRI ----> Tandem switch ----> Ottawa Office Server------+ +--------------> Lima Office Server -----+|