[R] Mismatch distribution

[Bert Gunter]

"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.croze07 using 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.croze07 using gmail.com
>
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>
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