You can use the functions in the ape package for this (where DNAbin is
defined).
To find the number of polymorphic sites, you can use the `seg.sites()`
function:
library(ape)
data(woodmouse)
length(seg.sites(woodmouse))
To expand the the fasta file, read it in as a DNAbin object and then use
the table with `rep()` to expand the indices in the matrix:
mytable <- data.frame(ids = names(woodmouse), n = sample(10,
nrow(woodmouse), rep = TRUE), stringsAsFactors = FALSE)
expanded_woodmouse <- woodmouse[with(mytable, rep(ids, n)), ]
Hope that helps,
Zhian
On 4/23/20 6:02 AM, Guillaume SCHWOB wrote:
Hello dear community,
I would have two questions:
The first one. I am looking for a way to count the number of polymorphic sites
across a DNAbin object in R ?
I was thinking about using the package Pegas, but I didn’t find any function
that could do that.
The second one. How can I expand a fasta file that contains unique sequences of
haplotypes according to a frequency table ?
I would be grateful to any guidance,
Best wishes,
Guillaume SCHWOB
Post Doctorado en Ecología Microbiana
Proyecto Genomics Antarctic Biodiversity (GAB)
Laboratorio de Ecología Molecular (LEM)
Departamento de Ciencias Ecológicas
Facultad de Ciencias, Universidad de Chile
Las Palmeras 3425,
CP 7800003, Ñuñoa, Santiago, Chile
http://www.antarcticgenomics.cl <http://www.antarcticgenomics.cl/>
https://www.researchgate.net/profile/Guillaume_Schwob
<https://www.researchgate.net/profile/Guillaume_Schwob>
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