similar to: Memory leak with character arrays?

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..

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

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 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 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! 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)

Hi, So far with the latest changes the projects I am trying to port works fine, except for a mismatch on what is considered the ansi behaviour of islower() in ctype.h: ----- i = 220 islower (i) = 0, ISLOWER (i) = 0 toupper (i) = 220, TOUPPER (i) = 220 i = 221 islower (i) = 0, ISLOWER (i) = 0 toupper (i) = 221, TOUPPER (i) = 221 i = 222 islower (i) = 0, ISLOWER (i) = 0 toupper (i) = 222, TOUPPER

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 return an index for a data set by searching using filenames. The name may be ANG_AUT.N.0734C70411A-1_1sA_0734C70411A.fasta, but i'd just like to search it using the term "0734C70411" as the file may be 0734C70411A or 0734C70411C or 0734C70411D Any way to do this other than doing something like this. where 0734C70411A is part of matrix list[,8]

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

> On 24 Oct 2017, at 22:45 , David L Carlson <dcarlson at tamu.edu> wrote: > > You left out all the most important bits of information. What is yo? Are you trying to assign a data frame to a single column in another data frame? Printing head(samples) tells us nothing about what data types you have, especially if the things that look like text are really factors that were created

Colleagues Assume that I have a vector containing some text strings, some of which contain a particular character. I could like to apply "toupper" to the text before the character. For example (in this case, "|" is the particular character): ORIGINAL: TEXT <- c("aaaa", "bbb|cc", "|ddd") AFTER APPLICATION OF toupper: TEXT <-

Hi Peter, Thanks for contributing such a great answer. Can you please provide a pointer to the documentation where it explains why dd$B <- s and dd["B"] <- s have such different behavior? (I am perfectly happy if you write the explanation but if it saves you time to point to some reference that works fine for me.) Regards, Eric On Wed, Oct 25, 2017 at 2:27 PM, Peter Dalgaard

Hi, I don't know what I am doing wrong to the toupper does not seem working in sub + regex. The following returns 's' not the upper class 'S' as I expect: sub("q_([a-z])[a-zA-Z]*",toupper('\\1'),"q_sviRaw") Can someone tell me where I did wrong? Thanks, Richard [[alternative HTML version deleted]]

You left out all the most important bits of information. What is yo? Are you trying to assign a data frame to a single column in another data frame? Printing head(samples) tells us nothing about what data types you have, especially if the things that look like text are really factors that were created when you used one of the read.*() functions. Use str(samples) to see what you are dealing with.

specifically, imagine we have: fooStack <- list() for ( i in 1:5 ) fooStack[[i]] <- list() and we have a function: fooModifier <- function( foo ) { foo$bar <- "bar" } then, if we invoke fooModifier, i.e.: fooModifier( fooStack[[ 1 ]] ) the $bar elt is only set in the scope of the function, and if we use the

Why doesn't this work? > samples$geno <- as.data.frame(sapply(yo, toupper), col.names="geno") > samples quant_samples age sapply(yo, toupper) E11.5 F20het BA40 E11.5 F20het BA40 E11.5 F20HET E11.5 F20het BA45 E11.5 F20het BA45 E11.5 F20HET

Wait. Now I'm really confused. > > head(samples) quant_samples age sapply(yo, toupper) E11.5 F20het BA40 E11.5 F20het BA40 E11.5 F20HET E11.5 F20het BA45 E11.5 F20het BA45 E11.5 F20HET E11.5 F20het BB84 E11.5 F20het BB84 E11.5 F20HET E11.5 F9.20DKO KTr3 E11.5 F9.20DKO KTr3 E11.5 F9.20DKO E11.5

Hi - I saw your posting on the R-help mailing list. Were you ever able to get this working? did you end up switching to use the rsge library? I'm trying to do the same, and not having very much luck getting it going. Thanks! Peter Waltman [[alternative HTML version deleted]]

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