[adegenet-forum] IBD distance matrices

[Thibaut Jombart]

Hi there,

yes, you can provide whatever 'dist' object you want to
ade4::mantel.randtest. If you start from a symmetric matrix coming from
another software, you can read it into R and convert it to dist using
'as.dist'.

Cheers
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
WHO Consultant - outbreak analysis
sites.google.com/site/thibautjombart/
Twitter: @TeebzR
+44(0)20 7594 3658

On 24 August 2017 at 20:22, Arsalan Emami-Khoyi <arsalan at pobox.com> wrote:

> Dear Thibut and Adegenet team,
> I would like to thank you for your contributions to the scientific
> community.
> I am estimating IBD for the same species using  three different data sets
> : mtDNA,microsatellie, and SNPs.
> For being consistent across the data sets we need to use appropriate
> distance matrices.
> I am wondering if there is any way to use our in-house distant matrices
> instead of provided distance measures?
> I will deeply appreciate your suggestions regarding the optimal distant
> method for each kind of data sets.
> Many thanks in advance and see you in October!
>
>
>
> Regards
>
> Arsalan Emami-Khoyi
> Postdoctoral Research Fellow in Wildlife Genomics
> University of Johannesburg_Center for Ecological Genomics and Wildlife
> Conservation
> Auckland Park 2006
> South Africa
> Email : Arsalane at uj.ac.za
> Phone :+27 (0)11 559 3373 <+27%2011%20559%203373>
> Cellphone:+27 79 88 14 628
> Website :https://sites.google.com/site/drpeterteske/postdocs
>
>
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