[adegenet-forum] Converting between adegenet and genetics

Fri Oct 9 17:32:11 CEST 2015

Hi Thibaut, and for future users,
I have found that the package poppr, which is highly compatable with adegenet, has a useful function for saving genind objects as csv files in genalex format. Genalex format can be converted to genepop and structure format at the flick of a swtich with the free GenAlex add on in Excel, and this add on has several handy features of it’s own.
Of course Thibaut is right, and R is a highly universal and wonderfully flexible program, but hopefully this info will help others to move outside of R if they need or prefer to.
Many thanks again for your help,
Robert
From: Jombart, Thibaut [mailto:t.jombart at imperial.ac.uk]
Sent: 09 October 2015 16:24
To: Robert Fairweather <osue37 at bangor.ac.uk>; adegenet-forum at lists.r-forge.r-project.org
Subject: RE: Converting between adegenet and genetics

Hi there,

genind2df will be helpful for recoding the data as allele, but then there will still be a way to go to export data for Genepop. As our purpose deveioping packages in R is to make R a single (free) platform for data analysis, I'd expect exporting data to other software is not going to be a priority for most developers.

Cheers
Thibaut
________________________________
From: Robert Fairweather [osue37 at bangor.ac.uk]
Sent: 09 October 2015 15:02
To: Jombart, Thibaut
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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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.

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