Myriam - This is the right list in principle, all the packages you use are CRAN packages, not Bioconductor.
However I am at a loss as to how you wrote your code: both pegas and seqinr have "read.<something>()" functions, but neither has read.dna(); similarly both pegas and seqinr have "dist.<something>()" functions, but neither has dist.gene(). Did you just extrapolate those function names and parameters from other function calls? In any case: please start from a minimal, reproducible example that comes close to what you are trying to achieve, then post again. Here are the three URLs we usually recommend to get things started. Use a small number of small example files, don't nest your expressions until you are sure they produce what you think they do, and take it step by step. http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example http://adv-r.had.co.nz/Reproducibility.html https://cran.r-project.org/web/packages/reprex/index.html (read the vignette) Cheers, B - > On 2019-01-21, at 21:08, Bert Gunter <bgunter.4...@gmail.com> wrote: > > "Do not work" does not work (in providing sufficient info). See the Posting > guide linked below for how to post an intelligible question. > > HOWEVER, I suspect you would do better posting on te Bioconductor list > where they are much more likely to know what "fasta" files look like and > might even have software already developed to do what you want. You could > well be trying to reinvent wheels. > > Cheers, > Bert > > > On Mon, Jan 21, 2019 at 5:35 PM Myriam Croze <myriam.croz...@gmail.com> > wrote: > >> Hello! >> >> I need your help. I am trying to calculate the pairwise differences between >> sequences from several fasta files. >> I would like for each of my DNA alignments (fasta files), calculate the >> pairwise differences and then: >> - 1. Combine all the data of each file to have one file and one histogram >> (mismatch distribution) >> - 2. calculate the mean for each difference for all the file and again make >> a mismatch distribution plot >> >> Here the script that I wrote: >> >> library("pegas") >>> library("seqinr") >>> library("ggplot2") >>> >>> >> >>> Files <- list.files(pattern="fas") >>> nb_files <- length(Files) >>> >>> >>> for (i in 1:nb_files) { >>> Dist <- as.numeric(dist.gene(read.dna(Files[i], "fasta"), method >>> = "pairwise", >>> pairwise.deletion = FALSE, variance = FALSE)) >>> >>> Data <- merge(Data, Dist, by=c("x"), all=T) >>> } >>> >> >> >>> hist(Data, prob=TRUE) >>> lines(density(Data), col="blue", lwd=2) >>> >> >> However, the script does not work and I do not know what to change to make >> it working. >> Thanks in advance for your help. >> >> Myriam >> >> -- >> Myriam Croze, PhD >> Post-doctorante >> Division of EcoScience, >> Ewha Womans University >> Seoul, South Korea >> >> Email: myriam.croz...@gmail.com >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
