Hi all! Hope you had a great summer!
I was wondering if anyone knew an R package able to load genetic data from .arp files (that is, the Arlequin input file format, http://cmpg.unibe.ch/software/arlequin35/Arlequin35.html)?
The R package strataG was able to do that (function read.arlequin) but is currently under maintenance (and was also removed from the CRAN) so cannot be used at the moment (and probably not before a few more weeks).
I will soon have a huge load of .arp simulated datasets generated from FastSimcoal and I would have been happy to process them through R, rather than arlsumstats (the console version of Arlequin), which apparently has trouble dealing with large simulated SNP datasets according to some users. I am also afraid that converting my .arp pseudo-datasets using PGDSpider (or any other conversion tool) might take a long while! We are talking of several thousands of pseudo-datasets, each one comprising genotypes from over 30,000 SNP loci.
Thank you very much for any suggestion, or any indication of an R package that could work :-)!
Cheers!
Chrys
I've used PGDSpider on large SNP datasets and it has worked well. To get a file format such as .arp into R it can involve several steps, such as using PGDSpider to create a VCF or PLINK file and then bring it into R.
A couple of R packages should be able to handle the .arp file directly. One of the most versatile is radiator (https://github.com/thierrygosselin/radiator). I think adegenet, which is available on CRAN, also can import .arp files.
Good luck!
Hi,
I have seen radiator has an option to export arlequin data but I can't see anything in the package to read .arp files? ie. write_arlequin .
Also Chrys, I am looking to calculated summary stats from .arp files from fastsimcoal too! I was going to use arlsumstat but I would much rather use R. Which R packages are you using to calculate summary statistics from your .arp files? There are so many options it is overwhelming!
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