[adegenet-forum] FW: Converting between adegenet and genetics

[Robert Fairweather]

Robert Fairweather
Research Student
Molecular Ecology and Fisheries Genetics Laboratory
Environment Centre Wales
Bangor Unversity
LL57 2UW

Email: osue37 at bangor.ac.uk<mailto:osue37 at bangor.ac.uk>
Skype: fairweathr
Twitter: @FairweathR

From: Robert Fairweather
Sent: 09 October 2015 15:02
To: 'Jombart, Thibaut' <t.jombart at imperial.ac.uk>
Subject: RE: Converting between adegenet and genetics

Dear Thibaut,
Many thanks for your response. Specifically I am trying to convert my genind object into genepop format so that I can use genetics to export it as a .gen file in said format. I have been getting the impression that support for genetics is waning across the board, and so am looking into alternative packages that may be able to save genepops and which adegenet can export to. Please do let me know if you know any. My data is co-dominant SNP data, originally imported into adegenet as a .gen file.
Cheers,
Robert

From: Jombart, Thibaut [mailto:t.jombart at imperial.ac.uk]
Sent: 09 October 2015 14:56
To: Robert Fairweather <osue37 at bangor.ac.uk<mailto:osue37 at bangor.ac.uk>>; adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
Subject: RE: Converting between adegenet and genetics

Dear Robert,

as of version 2.0.0, adegenet is no longer interfaced with the package genetics, but is meant to work with a number of others: hierfstat, pegas, poppr, ape, etc. I believe most functionalities implemented in genetics are implemented elsewhere, but please let me know if something is missing.

Cheers
Thibaut

________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org> [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Robert Fairweather [osue37 at bangor.ac.uk]
Sent: 09 October 2015 14:46
To: adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
Subject: [adegenet-forum] Converting between adegenet and genetics
Dear Thibaut,
I am trying to export a genind object from adegenet to genetics package format so that I can use functions in that package not available in adegenet. The adegenet homepage suggests that this is possible, but I cannot find anything in the instruction pdf detailing the appropriate function(s). An earlier post suggests the function genind2genotype, but this does not exist in the manual and cannot be found in the version of adegenet that I am using (2.0.0).
How can I export my genind object into genetics?
Best wishes,
Robert




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Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565

Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor.

This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

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