From medamato at gmail.com  Mon Apr  2 22:45:18 2018
From: medamato at gmail.com (Maria Eugenia D'Amato)
Date: Mon, 2 Apr 2018 22:45:18 +0200
Subject: [adegenet-forum] error message in the web server
Message-ID: <CA+xOXyM6emmvsQbxhezxPUNwetZtpXj=HMUSJ-zz0=BvWVi+Zw@mail.gmail.com>

* I tried the DAPC webserver after using the R version of DAPC, and I get
the following error message: unable to find an inherited method for
function ?tab? for signature ?"NULL"?*I  wrote the genind file I used in
the command line version as a .txt file and I get the above message when I
try to open it in the web server.
what and I doing wrong?
thnxalot
eugenia
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From roman.lustrik at biolitika.si  Tue Apr  3 07:45:50 2018
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Tue, 3 Apr 2018 07:45:50 +0200 (CEST)
Subject: [adegenet-forum] error message in the web server
In-Reply-To: <CA+xOXyM6emmvsQbxhezxPUNwetZtpXj=HMUSJ-zz0=BvWVi+Zw@mail.gmail.com>
References: <CA+xOXyM6emmvsQbxhezxPUNwetZtpXj=HMUSJ-zz0=BvWVi+Zw@mail.gmail.com>
Message-ID: <1348768295.1483710.1522734350206.JavaMail.zimbra@biolitika.si>

Please share the code you use to produce this error. 

Cheers, 
Roman 

---- 
In god we trust, all others bring data. 


From: "Maria Eugenia D'Amato" <medamato at gmail.com> 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Monday, April 2, 2018 10:45:18 PM 
Subject: [adegenet-forum] error message in the web server 

I tried the DAPC webserver after using the R version of DAPC, and I get the following error message: 
unable to find an inherited method for function ?tab? for signature ?"NULL"? 
I wrote the genind file I used in the command line version as a .txt file and I get the above message when I try to open it in the web server. 
what and I doing wrong? 
thnxalot 
eugenia 

_______________________________________________ 
adegenet-forum mailing list 
adegenet-forum at lists.r-forge.r-project.org 
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum 
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From taniachavarria79 at ufl.edu  Tue Apr  3 18:40:27 2018
From: taniachavarria79 at ufl.edu (Chavarria,Tania)
Date: Tue, 3 Apr 2018 16:40:27 +0000
Subject: [adegenet-forum] Bug report
Message-ID: <BN6PR2201MB110812D54C88C4C43C366F34D7A50@BN6PR2201MB1108.namprd22.prod.outlook.com>

Hello,

I think there is a bug in the adeneget program! I was using it before this morning and now I can not run the script I did install it again and it shows this message:

Error in library.dynam(lib, package, package.lib) :
  shared object 'stringi.so' not found
ERROR: lazy loading failed for package 'adegenet'
* removing '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/adegenet'
* restoring previous '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/adegenet'
Installation failed: Command failed (1)



If there is not a bug, i do not know what happen? I did re-install again my R software and I still get this message


Thanks!
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From shripathipn at yahoo.co.in  Wed Apr  4 16:49:16 2018
From: shripathipn at yahoo.co.in (shripathi bhat)
Date: Wed, 4 Apr 2018 14:49:16 +0000 (UTC)
Subject: [adegenet-forum] error using snapclust
References: <1034986377.1719125.1522853356105.ref@mail.yahoo.com>
Message-ID: <1034986377.1719125.1522853356105@mail.yahoo.com>

Hi, I was trying to apply snapclust function on my genind object (from structure input file). Here I used prior K and pop.ini was factor of pop id? (numbers) for all individuals.? snapclust initially reads the geneind object and then exits with error? "Error in t(ll)[cbind(seq_along(group), as.integer(group))] : subscript out of bounds".? I tried to google,? but no luck. snapclust works perfectly when I use it with find.clusters (pop.ini =geneindobject$grp),


?With regards, 
Shri

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From thibautjombart at gmail.com  Wed Apr  4 17:52:50 2018
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Wed, 4 Apr 2018 16:52:50 +0100
Subject: [adegenet-forum] Bug report
In-Reply-To: <BN6PR2201MB110812D54C88C4C43C366F34D7A50@BN6PR2201MB1108.namprd22.prod.outlook.com>
References: <BN6PR2201MB110812D54C88C4C43C366F34D7A50@BN6PR2201MB1108.namprd22.prod.outlook.com>
Message-ID: <CANPRA+pYEc8AqPwze1QJke1HCEmWvvZkP-Kgpp_9Gip85f7tdw@mail.gmail.com>

Hi Tania,

bugs are best reported on github using the issue system:
https://github.com/thibautjombart/adegenet

In this case, it sounds like stringi is merely missing. Can you try:
install.packages("stringi")
install.packages("adegenet")
library("adegenet")

Cheers
Thibaut


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

On 3 April 2018 at 17:40, Chavarria,Tania <taniachavarria79 at ufl.edu> wrote:

> Hello,
>
> I think there is a bug in the adeneget program! I was using it before this
> morning and now I can not run the script I did install it again and it
> shows this message:
>
> Error in library.dynam(lib, package, package.lib) :
>   shared object 'stringi.so' not found
> ERROR: lazy loading failed for package 'adegenet'
> * removing '/Library/Frameworks/R.framework/Versions/3.3/
> Resources/library/adegenet'
> * restoring previous '/Library/Frameworks/R.framework/Versions/3.3/
> Resources/library/adegenet'
> Installation failed: Command failed (1)
>
>
> If there is not a bug, i do not know what happen? I did re-install again
> my R software and I still get this message
>
>
> Thanks!
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/
> listinfo/adegenet-forum
>
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From thibautjombart at gmail.com  Wed Apr  4 17:54:18 2018
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Wed, 4 Apr 2018 16:54:18 +0100
Subject: [adegenet-forum] Add XY axes and labels to s.class or
 scatter.dapc PCA plot
In-Reply-To: <7963D83B-1C94-4940-8C54-D4A5DD13673C@princeton.edu>
References: <7963D83B-1C94-4940-8C54-D4A5DD13673C@princeton.edu>
Message-ID: <CANPRA+qdNvJ+e5j7P7EqckHqs=xSsBDocZZXgnuhcODPyrnOpQ@mail.gmail.com>

Hi there,

scatter.dapc should only be used for dapc objects.

For further customisation of s.class graphics, I would recommend using
adegraphics:
https://cran.r-project.org/web/packages/adegraphics/vignettes/adegraphics.html

Best
Thibaut


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

On 29 March 2018 at 17:27, Daniel T. Baldassarre <danieltb at princeton.edu>
wrote:

> Hello,
>
> I have a ?genind' object with genotyped individuals assigned to known
> populations. I?m using ?s.class' and ?scatter.dapc' to produce PCA plots
> where the individuals are colored by population. This works without any
> issue and produces beautiful plots, but I?m wondering if there is a way to
> add values and labels to the XY axes as is done in, for example,
> ?colorplot?.
>
> Thanks!
>
> ---
> Daniel T. Baldassarre
>
> Postdoctoral Research Associate
> Riehl Lab, Dept of Eco and Evo Bio
> Princeton University
> 106A Guyot Hall
> Princeton, NJ 08544
> 609-258-4919
> danbaldassarre.weebly.com
>
>
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/
> listinfo/adegenet-forum
>
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From roman.lustrik at biolitika.si  Wed Apr  4 19:52:04 2018
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Wed, 4 Apr 2018 19:52:04 +0200 (CEST)
Subject: [adegenet-forum] error using snapclust
In-Reply-To: <1034986377.1719125.1522853356105@mail.yahoo.com>
References: <1034986377.1719125.1522853356105.ref@mail.yahoo.com>
 <1034986377.1719125.1522853356105@mail.yahoo.com>
Message-ID: <1017897377.1491591.1522864324868.JavaMail.zimbra@biolitika.si>

Hi, 

it would be best if you could provide a reproducible example (data, code). 

Cheers, 
Roman 

---- 
In god we trust, all others bring data. 


From: "shripathi bhat" <shripathipn at yahoo.co.in> 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Wednesday, April 4, 2018 4:49:16 PM 
Subject: [adegenet-forum] error using snapclust 

Hi, 
I was trying to apply snapclust function on my genind object (from structure input file). Here I used prior K and pop.ini was factor of pop id (numbers) for all individuals. snapclust initially reads the geneind object and then exits with error " Error in t(ll)[cbind(seq_along(group), as.integer(group))] : subscript out of bounds". I tried to google, but no luck. snapclust works perfectly when I use it with find.clusters (pop.ini =geneindobject$grp), 


With regards, 
Shri 


_______________________________________________ 
adegenet-forum mailing list 
adegenet-forum at lists.r-forge.r-project.org 
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum 
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From fayyaz.farzad at gmail.com  Thu Apr  5 19:12:18 2018
From: fayyaz.farzad at gmail.com (Farzad Fayyaz)
Date: Thu, 5 Apr 2018 21:42:18 +0430
Subject: [adegenet-forum] data analysis by DAPC
Message-ID: <CAMDu66CAYo+=ChwS3sBrOJHEszApFi-2ihP6S_LrCH7rUx4W-w@mail.gmail.com>

 Hello Dear,
I have 1500 DArT markers(0 or 1 data) on durum wheat crop, and I need to
investigate structure and genetic diversity parameters by DCPA technique.
Please inform me with how to crate data file input for analysis in R
software.


Sincerely
Fayaz-Farzad

-- 
Farzad Fayaz
Assistant professor
Dept. Plant Breeding & Agronomy
Islamic Azad University, Sanandaj Branch
Sanandaj, Iran.
P.O.Box:618
Tel:0098-9183731867, 0098-8733237047
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From thibautjombart at gmail.com  Thu Apr  5 19:39:30 2018
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Thu, 5 Apr 2018 18:39:30 +0100
Subject: [adegenet-forum] data analysis by DAPC
In-Reply-To: <CAMDu66CAYo+=ChwS3sBrOJHEszApFi-2ihP6S_LrCH7rUx4W-w@mail.gmail.com>
References: <CAMDu66CAYo+=ChwS3sBrOJHEszApFi-2ihP6S_LrCH7rUx4W-w@mail.gmail.com>
Message-ID: <CANPRA+pZzBwsK3UdoqOckCvV-n6P9QgVGB_4NcCCXW1UvQ2vOw@mail.gmail.com>

Hi there,

as I replied in private, please check out the doc before asking questions,
especially in this case the basics tutorial for data import, and the DAPC
tutorial.

https://github.com/thibautjombart/adegenet/wiki/Tutorials

Cheers
Thibaut


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

On 5 April 2018 at 18:12, Farzad Fayyaz <fayyaz.farzad at gmail.com> wrote:

> Hello Dear,
> I have 1500 DArT markers(0 or 1 data) on durum wheat crop, and I need to
> investigate structure and genetic diversity parameters by DCPA technique.
> Please inform me with how to crate data file input for analysis in R
> software.
>
>
> Sincerely
> Fayaz-Farzad
>
> --
> Farzad Fayaz
> Assistant professor
> Dept. Plant Breeding & Agronomy
> Islamic Azad University, Sanandaj Branch
> Sanandaj, Iran.
> P.O.Box:618
> Tel:0098-9183731867, 0098-8733237047
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/
> listinfo/adegenet-forum
>
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From medamato at gmail.com  Sun Apr  8 22:33:49 2018
From: medamato at gmail.com (Maria Eugenia D'Amato)
Date: Sun, 8 Apr 2018 22:33:49 +0200
Subject: [adegenet-forum] error message in the web server
In-Reply-To: <1348768295.1483710.1522734350206.JavaMail.zimbra@biolitika.si>
References: <CA+xOXyM6emmvsQbxhezxPUNwetZtpXj=HMUSJ-zz0=BvWVi+Zw@mail.gmail.com>
 <1348768295.1483710.1522734350206.JavaMail.zimbra@biolitika.si>
Message-ID: <CA+xOXyPSGi0QiycicQTsm9Ez=sFeJ4GrL_t9o_X9n=RpRLoO+A@mail.gmail.com>

Hello Roman,

Thanks for your email, finally I managed to solve the problem myself:
I was working in RStudio and after converting my haploid data to a genind
object, I was trying to save it as a file for further use in the DAPC
webserver.
I was using the wrong code, I was trying to write a table from a genind
object, as csv.
But then, did the following:

*save(Ugenind1, file = "Ugenind1.Rdata")*

which worked !

I am new to R and adegenet :)

best,

eugenia




On Tue, Apr 3, 2018 at 7:45 AM, Roman Lu?trik <roman.lustrik at biolitika.si>
wrote:

> Please share the code you use to produce this error.
>
> Cheers,
> Roman
>
> ----
> In god we trust, all others bring data.
>
> ------------------------------
> *From: *"Maria Eugenia D'Amato" <medamato at gmail.com>
> *To: *adegenet-forum at lists.r-forge.r-project.org
> *Sent: *Monday, April 2, 2018 10:45:18 PM
> *Subject: *[adegenet-forum] error message in the web server
>
> * I tried the DAPC webserver after using the R version of DAPC, and I get
> the following error message: unable to find an inherited method for
> function ?tab? for signature ?"NULL"?*I  wrote the genind file I used in
> the command line version as a .txt file and I get the above message when I
> try to open it in the web server.
> what and I doing wrong?
> thnxalot
> eugenia
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/
> listinfo/adegenet-forum
>
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From roman.lustrik at biolitika.si  Mon Apr  9 07:20:53 2018
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Mon, 9 Apr 2018 07:20:53 +0200 (CEST)
Subject: [adegenet-forum] error message in the web server
In-Reply-To: <CA+xOXyPSGi0QiycicQTsm9Ez=sFeJ4GrL_t9o_X9n=RpRLoO+A@mail.gmail.com>
References: <CA+xOXyM6emmvsQbxhezxPUNwetZtpXj=HMUSJ-zz0=BvWVi+Zw@mail.gmail.com>
 <1348768295.1483710.1522734350206.JavaMail.zimbra@biolitika.si>
 <CA+xOXyPSGi0QiycicQTsm9Ez=sFeJ4GrL_t9o_X9n=RpRLoO+A@mail.gmail.com>
Message-ID: <585354353.1500870.1523251253850.JavaMail.zimbra@biolitika.si>

Glad you were able to sort the issue out. This is why it's important to create aminimal working example, even if just for yourself. It forces you that you understand the process enough to make it work. 

Cheers, 
Roman 

---- 
In god we trust, all others bring data. 


From: "Maria Eugenia D'Amato" <medamato at gmail.com> 
To: "Roman Lu?trik" <roman.lustrik at biolitika.si> 
Cc: adegenet-forum at lists.r-forge.r-project.org 
Sent: Sunday, April 8, 2018 10:33:49 PM 
Subject: Re: [adegenet-forum] error message in the web server 

Hello Roman, 

Thanks for your email, finally I managed to solve the problem myself: 
I was working in RStudio and after converting my haploid data to a genind object, I was trying to save it as a file for further use in the DAPC webserver. 
I was using the wrong code, I was trying to write a table from a genind object, as csv. 
But then, did the following: 



save(Ugenind1, file = "Ugenind1.Rdata") 

which worked ! 


I am new to R and adegenet :) 


best, 

eugenia 





On Tue, Apr 3, 2018 at 7:45 AM, Roman Lu?trik < roman.lustrik at biolitika.si > wrote: 



Please share the code you use to produce this error. 

Cheers, 
Roman 

---- 
In god we trust, all others bring data. 


From: "Maria Eugenia D'Amato" < medamato at gmail.com > 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Monday, April 2, 2018 10:45:18 PM 
Subject: [adegenet-forum] error message in the web server 

I tried the DAPC webserver after using the R version of DAPC, and I get the following error message: 
unable to find an inherited method for function ?tab? for signature ?"NULL"? 
I wrote the genind file I used in the command line version as a .txt file and I get the above message when I try to open it in the web server. 
what and I doing wrong? 
thnxalot 
eugenia 

_______________________________________________ 
adegenet-forum mailing list 
adegenet-forum at lists.r-forge.r-project.org 
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum 




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From Mark.Coulson.ic at uhi.ac.uk  Thu Apr 12 16:17:01 2018
From: Mark.Coulson.ic at uhi.ac.uk (Mark Coulson)
Date: Thu, 12 Apr 2018 14:17:01 +0000
Subject: [adegenet-forum] resampling individuals from genind
Message-ID: <DB5PR06MB095100ACCC62CC238381313CEABC0@DB5PR06MB0951.eurprd06.prod.outlook.com>

I have a genind object with ~40 populations of varying sample sizes. I want to take 20 of these groups and sample 10 individuals at random (without replacement) from each of these 20 populations into a new group (which will end up being 200 individuals). I can't quite figure out how to best do this. Does it require seppop? If so then how do I avoid specifying a draw of twenty individual for each individually separate population?

Thanks
Mark

Inverness College UHI, a partner in the University of the Highlands and Islands www.inverness.uhi.ac.uk Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.
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From 03ledg at gmail.com  Thu Apr 12 19:49:43 2018
From: 03ledg at gmail.com (Luz Elena De La Ossa Guerra)
Date: Thu, 12 Apr 2018 14:49:43 -0300
Subject: [adegenet-forum] Data input in IBD
Message-ID: <CAGmhCUHk9GFSp1vHWX4HrvgE2uW4_ofX9JEPdT_2Fo7uzcdWqA@mail.gmail.com>

Hi everybody,

I am new in adegenet, I am doing Isolation by distance analysis, but I am
wondering if some of you can tell me how I do the data input. They are
genetic distance and geographic distance between groups, but i don?t know
how they are organized. If someone can send me an example, or where could I
find it I would be grateful.

Thank you.

-- 
*Luz E. De la Ossa Guerra*
*Biolog?a*
*Universidad de Sucre*
?
[image: Mailtrack]
<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality1&>
Enviado
con Mailtrack
<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality1&>
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From garycharleslongo at gmail.com  Fri Apr 13 01:09:34 2018
From: garycharleslongo at gmail.com (Gary Longo)
Date: Thu, 12 Apr 2018 16:09:34 -0700
Subject: [adegenet-forum] different results for pegas and hierfstat Fst via
	weir and cockerham
Message-ID: <CANjmwbHieEAoifXLixi_9JRYZ3BQHR7VqFqOp=4S1W3H=ktEmg@mail.gmail.com>

Hi Thibaut and company!

# I've noticed differences with Fst and Fis calculations in Pegas vs
Hierfstat while using Adegenet

> data("nancycats")

# using weir and cockerham in pegas
> nancycats_Fstat_as_loci <- Fst(as.loci(nancycats))
> nancycats_Fstat_as_loci

            Fit        Fst         Fis
fca8  0.2447420 0.10146648 0.159454807
fca23 0.1646295 0.06746762 0.104191391
fca43 0.1514487 0.06893755 0.088620458
fca45 0.1010807 0.09792456 0.003498722
fca77 0.2790495 0.10036588 0.198618075
fca78 0.1842490 0.07025915 0.122603911
fca90 0.2098744 0.09168833 0.130116240
fca96 0.2034755 0.10744024 0.107595351
fca37 0.2604033 0.06985321 0.204860244

# also using weir & cockerham in hierfstat
> nancycats_hfstat <- genind2hierfstat(nancycats)
> nancycats_wc <- wc(nancycats_hfstat)
> nancycats_wc_loci_stats <- as.data.frame(nancycats_wc[["per.loc"]])
> nancycats_wc_loci_stats

         FST          FIS
1 0.10150515  0.148673460
2 0.06746762  0.104191391
3 0.06893755  0.088620458
4 0.07652596 -0.001451681
5 0.10036588  0.198618075
6 0.07025915  0.122603911
7 0.09168833  0.130116240
8 0.10981110  0.094857474
9 0.06985321  0.204860244


> colSums(is.na(nancycats_hfstat))

  pop  fca8 fca23 fca43 fca45 fca77 fca78 fca90 fca96 fca37
    0    20     0     0    21     0     0     0     9     0


The results are identical in loci that are not missing data but are
different in loci with missing data.

Two questions:
1) How are they handling missing data differently since they are both using
Weir and Cockerham 1984? Follow up: which is better suited for calculating
Fst and Fis values when there are missing data? I'm analyzing a SNP dataset
based on ~2100 RADseq loci in over 500 individuals, which of course has
some missing data at most loci. My results from calculating these values in
Pegas vs Hierfstat are very different. Specifically Fst and Fis values are
generally much higher and I don't get any negative Fis values when
calculated in pegas.

2) Why does the conversion to hierfstat result in the loss of loci name?
This would be very useful to retain for downstream comparisons.

Cheers,
Gary


-- 
Gary Charles Longo
NRC Research Associate
NOAA, National Marine Fisheries Service
2725 Montlake Blvd E
Seattle, WA  98112
garycharleslongo.wordpress.com
(831) 247-3056
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From reige012 at gmail.com  Fri Apr 13 17:10:31 2018
From: reige012 at gmail.com (Alicia Reigel)
Date: Fri, 13 Apr 2018 10:10:31 -0500
Subject: [adegenet-forum] DAPC- Coloring Points by Source Population,
 but Group Point by Genetic Cluster
Message-ID: <CAGcVJpbboetjedTeysTzB+zcsaTmCH31Y=Oi-5qGNgVSaSOMDg@mail.gmail.com>

Hello,

I'm having some trouble working through an issue in DAPC. I've been using
scatter and DAPC to plot my points from microsatellite data. I have
definitely figured out how to cluster and color the points for the
individuals by their genetic cluster and by their original populations, but
what I can't determine is how to color each point by the original source
population, but cluster them by their genetic cluster.  Can anyone help me
with this?

Thanks,
Alicia Reigel

-- 
Ph.D. Candidate, Louisiana State University | Michael E.Hellberg Lab
M.S. Biology, Georgia Southern University | Daniel F. Gleason Lab
Lab Phone: (225) 578-9114
Email: areige1 at lsu.edu
Website: aliciamreigel.wordpress.com
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From thibautjombart at gmail.com  Mon Apr 16 13:23:06 2018
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Mon, 16 Apr 2018 12:23:06 +0100
Subject: [adegenet-forum] Data input in IBD
In-Reply-To: <CAGmhCUHk9GFSp1vHWX4HrvgE2uW4_ofX9JEPdT_2Fo7uzcdWqA@mail.gmail.com>
References: <CAGmhCUHk9GFSp1vHWX4HrvgE2uW4_ofX9JEPdT_2Fo7uzcdWqA@mail.gmail.com>
Message-ID: <CANPRA+r+4gr82=tN2zutr1kgxuRBo6fa=qZ26zgZ9EaOe=_XZQ@mail.gmail.com>

Hello,

please have a look at the basics tutorial, this is all documented there.
https://github.com/thibautjombart/adegenet/wiki/Tutorials

Cheers
Thibaut


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

On 12 April 2018 at 18:49, Luz Elena De La Ossa Guerra <03ledg at gmail.com>
wrote:

> Hi everybody,
>
> I am new in adegenet, I am doing Isolation by distance analysis, but I am
> wondering if some of you can tell me how I do the data input. They are
> genetic distance and geographic distance between groups, but i don?t know
> how they are organized. If someone can send me an example, or where could I
> find it I would be grateful.
>
> Thank you.
>
> --
> *Luz E. De la Ossa Guerra*
> *Biolog?a*
> *Universidad de Sucre*
> ?
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality1&> Enviado
> con Mailtrack
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality1&>
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/
> listinfo/adegenet-forum
>
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From thibautjombart at gmail.com  Mon Apr 16 14:06:25 2018
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Mon, 16 Apr 2018 13:06:25 +0100
Subject: [adegenet-forum] resampling individuals from genind
In-Reply-To: <DB5PR06MB095100ACCC62CC238381313CEABC0@DB5PR06MB0951.eurprd06.prod.outlook.com>
References: <DB5PR06MB095100ACCC62CC238381313CEABC0@DB5PR06MB0951.eurprd06.prod.outlook.com>
Message-ID: <CANPRA+ow76OzcLyPjm-M73rF=ZreAxu4mp_F3rbnWRP8Qba++w@mail.gmail.com>

Hi Mark,

I wonder if there isn't a function doing just that in poppr, but here's a
simple way to do it using microbov:

## subset 10 pop (I can't use 20 here)
x <- microbov[pop = sample(seq_len(nPop(microbov)), 10)]

## sample individuals with replacement - here, 5 per pop
sampled_indiv <-  unlist(tapply(seq_len(nInd(x)), pop(x), sample, size = 5,
replace = TRUE))
new_data <- x[sampled_indiv]

Cheers
Thibaut


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

On 12 April 2018 at 15:17, Mark Coulson <Mark.Coulson.ic at uhi.ac.uk> wrote:

> I have a genind object with ~40 populations of varying sample sizes. I
> want to take 20 of these groups and sample 10 individuals at random
> (without replacement) from each of these 20 populations into a new group
> (which will end up being 200 individuals). I can?t quite figure out how to
> best do this. Does it require seppop? If so then how do I avoid specifying
> a draw of twenty individual for each individually separate population?
>
>
>
> Thanks
>
> Mark
>
>
> Inverness College UHI, a partner in the University of the Highlands and
> Islands www.inverness.uhi.ac.uk Board of Management of Inverness College
> (known as Inverness College UHI), Scottish Charity No SC021197.
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/
> listinfo/adegenet-forum
>
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From lucia.maffey at gmail.com  Mon Apr 16 21:00:20 2018
From: lucia.maffey at gmail.com (Lu Maffey)
Date: Mon, 16 Apr 2018 16:00:20 -0300
Subject: [adegenet-forum] problem with DAPC/find clusters analyses with rad
	seq data
Message-ID: <CALJ95SQw6ddwSSGdh0FZmi7zT3ED-LcSC_u-2zKw2912ZW9QkQ@mail.gmail.com>

Hi Thibaut and everyone!

I need some help with a DAPC analyses I'm trying to perform on my radseq
data (whole genome for different mosquitoe samples, total of 65
individuals). (I'm new with Adegenet so I apologize in advance if this
question is quite basic!). The samples are from different locations and I'm
trying to stablish if there is population structure within the data. I have
previously performed analyses using Structure which showed that there are
different clusters (of course using fewer SNPs than the total number
available because of the panmixia assumption). So I've created the genlight
object with all the SNPs(after filtering low frequencies in plink) but when
I use find.clusters, the BIC against number of clusters graph only shows
increasing values of BIC. It never decreases. So I know that it's not the
only way to determine the number of clusters to perform the analysis but
I'm not sure wether this means that the program doesn't recognize any
clusters within the data or some other issue. I've tried using the same
value I've obtained for this data in Structure and it shows a similar
asignation but I'm not sure if thisis correct.
If I perform a DAPC analyses, when I use the scatter function to show the
results, the graph only shows the groups numbers, but no individual dots.
Could you please give me some insight about what's going on here?

Thank you very much in advance!

cheers

Lu
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From abelasen at umich.edu  Wed Apr 18 03:35:49 2018
From: abelasen at umich.edu (Anat Belasen)
Date: Tue, 17 Apr 2018 21:35:49 -0400
Subject: [adegenet-forum] issues with genind object for MHC supertyping
Message-ID: <CAD6JuTBuDi3wXuf_UOKp8qpuO7wYLkugNKgUdL7DjJ35GB1BEQ@mail.gmail.com>

Hello,

I have been trying to follow the example of many MHC studies that use DAPC
in adegenet to determine clusters/supertypes. According to what I've read,
I need to use a matrix of the physicochemical properties of the amino acids
in my MHC sequences to determine clustering. However, I can't get R to
accept this matrix as a genind object. I have been able to turn it into a
loci object but the loci2genind function returns an error:

Error in .local(.Object, ...) :
  more than one '.' in column names; please name column as [LOCUS].[ALLELE]

I have tried removing headers, changing the headers so they do resemble the
"locus.allele" format, and nothing seems to work. I'm not sure if this is
because this isn't a matrix of 0's and 1's (but rather values that include
decimals and sometimes are negative).

Can you advise how to proceed with this dataset? Perhaps is there an
example dataset used for this purpose?

Thank you,

Anat

-- 
-- 
Anat Belasen (personal website <https://anatbelasen.weebly.com/>)
M.S., Natural Resources and Environment 2013
<https://sites.google.com/a/umich.edu/foufopoulos/people/former-graduate-postgraduate-students>
PhD Candidate, Ecology & Evolutionary Biology
<http://www.umich.edu/~mycology/people.html>
FEMMES <http://femmes.studentorgs.umich.edu/> Secretary 2017-2018
University of Michigan
Ann Arbor, MI
@anatinmyshoe <https://twitter.com/anatinmyshoe>
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From mkonop at wp.pl  Wed Apr 18 17:10:18 2018
From: mkonop at wp.pl (Maciek)
Date: Wed, 18 Apr 2018 17:10:18 +0200
Subject: [adegenet-forum] Coordinates and distances in sPCA
In-Reply-To: <CANPRA+oLiq534F-+7-Qs_QE3kZc5_oB+7WfYuGuqs8_fywoy6w@mail.gmail.com>
References: <CANPRA+oLiq534F-+7-Qs_QE3kZc5_oB+7WfYuGuqs8_fywoy6w@mail.gmail.com>
Message-ID: <6257b1a5-9778-993b-49a4-8480d40547f2@wp.pl>

Dear All,

I've searched tutorials and internet to find what coordinate system 
should be used in sPCA but found no information. I checked data from 
Rupica, but could not figure out what cooridinate system it is. When I 
used regular WGS84 coordinates the distances between points are 
expressed in strange units of approximatelly 78 km but are consistent 
along north/south and east/west distances (however I did not check them 
in detail).

Where should I search for such information?

Cheers,

Maciek


From mstagliamonte at ufl.edu  Wed Apr 18 17:14:58 2018
From: mstagliamonte at ufl.edu (Tagliamonte,Massimiliano S)
Date: Wed, 18 Apr 2018 15:14:58 +0000
Subject: [adegenet-forum] Coordinates and distances in sPCA
In-Reply-To: <6257b1a5-9778-993b-49a4-8480d40547f2@wp.pl>
References: <CANPRA+oLiq534F-+7-Qs_QE3kZc5_oB+7WfYuGuqs8_fywoy6w@mail.gmail.com>,
 <6257b1a5-9778-993b-49a4-8480d40547f2@wp.pl>
Message-ID: <1524064498394.81978@ufl.edu>

Dear Maciek,

If I remember correctly, you need to use the UTM coordinate system. I do not have access to my personal computer right now, so you'll have to do some search to find the appropriate conversion programs or packages, it's been some time since I last did it. Feel free to write again if you need any more details.

Regards,
Max

Massimiliano S. Tagliamonte
DVM, MSc, PhD
Postdoc Associate
Emerging Pathogens Institute
Department of Pathology
College of Medicine
University of Florida

________________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at <adegenet-forum-bounces at r-forge.wu-wien.ac.at> on behalf of Maciek <mkonop at wp.pl>
Sent: Wednesday, April 18, 2018 11:10 AM
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] Coordinates and distances in sPCA

Dear All,

I've searched tutorials and internet to find what coordinate system
should be used in sPCA but found no information. I checked data from
Rupica, but could not figure out what cooridinate system it is. When I
used regular WGS84 coordinates the distances between points are
expressed in strange units of approximatelly 78 km but are consistent
along north/south and east/west distances (however I did not check them
in detail).

Where should I search for such information?

Cheers,

Maciek

_______________________________________________
adegenet-forum mailing list
adegenet-forum at lists.r-forge.r-project.org
https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.r-2Dforge.r-2Dproject.org_cgi-2Dbin_mailman_listinfo_adegenet-2Dforum&d=DwICAg&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=VKMSeIT5HKvjRErWI8R0zntMm_kPWBrZQJU4mlHwsIA&m=3gqPYp35vSvHM-XBpjQ3azNlqgP5MwUR8_2yksZj3oA&s=xUFAx7aTbxmpoRrWI7j4SMwRTpO92DCZuWY_pZdioXg&e=

From mstagliamonte at ufl.edu  Wed Apr 18 17:21:39 2018
From: mstagliamonte at ufl.edu (Tagliamonte,Massimiliano S)
Date: Wed, 18 Apr 2018 15:21:39 +0000
Subject: [adegenet-forum] Coordinates and distances in sPCA
In-Reply-To: <6257b1a5-9778-993b-49a4-8480d40547f2@wp.pl>
References: <CANPRA+oLiq534F-+7-Qs_QE3kZc5_oB+7WfYuGuqs8_fywoy6w@mail.gmail.com>,
 <6257b1a5-9778-993b-49a4-8480d40547f2@wp.pl>
Message-ID: <1524064899474.91121@ufl.edu>

I am not sure the previous message was sent correctly, so I will try again:

If I remember correctly,  you should convert your coordinates to the utm system. I do not have access to my old scripts right now, so you'll have to look for some converter package. Let me know if you need any more help with it.

Regards,
Max

Massimiliano S. Tagliamonte
DVM, MSc, PhD
Postdoc Associate
Emerging Pathogens Institute
Department of Pathology
College of Medicine
University of Florida

________________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at <adegenet-forum-bounces at r-forge.wu-wien.ac.at> on behalf of Maciek <mkonop at wp.pl>
Sent: Wednesday, April 18, 2018 11:10 AM
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] Coordinates and distances in sPCA

Dear All,

I've searched tutorials and internet to find what coordinate system
should be used in sPCA but found no information. I checked data from
Rupica, but could not figure out what cooridinate system it is. When I
used regular WGS84 coordinates the distances between points are
expressed in strange units of approximatelly 78 km but are consistent
along north/south and east/west distances (however I did not check them
in detail).

Where should I search for such information?

Cheers,

Maciek

_______________________________________________
adegenet-forum mailing list
adegenet-forum at lists.r-forge.r-project.org
https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.r-2Dforge.r-2Dproject.org_cgi-2Dbin_mailman_listinfo_adegenet-2Dforum&d=DwICAg&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=VKMSeIT5HKvjRErWI8R0zntMm_kPWBrZQJU4mlHwsIA&m=3gqPYp35vSvHM-XBpjQ3azNlqgP5MwUR8_2yksZj3oA&s=xUFAx7aTbxmpoRrWI7j4SMwRTpO92DCZuWY_pZdioXg&e=

From mkonop at wp.pl  Wed Apr 18 17:21:51 2018
From: mkonop at wp.pl (mkonop at wp.pl)
Date: Wed, 18 Apr 2018 17:21:51 +0200
Subject: [adegenet-forum] Coordinates and distances in sPCA
In-Reply-To: <1524064498394.81978@ufl.edu>
References: <CANPRA+oLiq534F-+7-Qs_QE3kZc5_oB+7WfYuGuqs8_fywoy6w@mail.gmail.com>
 <6257b1a5-9778-993b-49a4-8480d40547f2@wp.pl> <1524064498394.81978@ufl.edu>
Message-ID: <9345ACEA-864F-484F-BF01-3F287482CE14@wp.pl>

Dear Massimiliano,
Thanks for quick answer. The problem with UTM and my data is that my samples are in 3 or even 4 UTM zones. I did not find a way to transform such a big area to UTM coordinates. 

Maciek

> Wiadomo?? napisana przez Tagliamonte,Massimiliano S <mstagliamonte at ufl.edu> w dniu 18.04.2018, o godz. 17:14:
> 
> Dear Maciek,
> 
> If I remember correctly, you need to use the UTM coordinate system. I do not have access to my personal computer right now, so you'll have to do some search to find the appropriate conversion programs or packages, it's been some time since I last did it. Feel free to write again if you need any more details.
> 
> Regards,
> Max
> 
> Massimiliano S. Tagliamonte
> DVM, MSc, PhD
> Postdoc Associate
> Emerging Pathogens Institute
> Department of Pathology
> College of Medicine
> University of Florida
> 
> ________________________________________
> From: adegenet-forum-bounces at r-forge.wu-wien.ac.at <adegenet-forum-bounces at r-forge.wu-wien.ac.at> on behalf of Maciek <mkonop at wp.pl>
> Sent: Wednesday, April 18, 2018 11:10 AM
> To: adegenet-forum at r-forge.wu-wien.ac.at
> Subject: [adegenet-forum] Coordinates and distances in sPCA
> 
> Dear All,
> 
> I've searched tutorials and internet to find what coordinate system
> should be used in sPCA but found no information. I checked data from
> Rupica, but could not figure out what cooridinate system it is. When I
> used regular WGS84 coordinates the distances between points are
> expressed in strange units of approximatelly 78 km but are consistent
> along north/south and east/west distances (however I did not check them
> in detail).
> 
> Where should I search for such information?
> 
> Cheers,
> 
> Maciek
> 
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.r-2Dforge.r-2Dproject.org_cgi-2Dbin_mailman_listinfo_adegenet-2Dforum&d=DwICAg&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=VKMSeIT5HKvjRErWI8R0zntMm_kPWBrZQJU4mlHwsIA&m=3gqPYp35vSvHM-XBpjQ3azNlqgP5MwUR8_2yksZj3oA&s=xUFAx7aTbxmpoRrWI7j4SMwRTpO92DCZuWY_pZdioXg&e=


From mstagliamonte at ufl.edu  Wed Apr 18 17:30:25 2018
From: mstagliamonte at ufl.edu (Tagliamonte,Massimiliano S)
Date: Wed, 18 Apr 2018 15:30:25 +0000
Subject: [adegenet-forum] Coordinates and distances in sPCA
In-Reply-To: <9345ACEA-864F-484F-BF01-3F287482CE14@wp.pl>
References: <CANPRA+oLiq534F-+7-Qs_QE3kZc5_oB+7WfYuGuqs8_fywoy6w@mail.gmail.com>
 <6257b1a5-9778-993b-49a4-8480d40547f2@wp.pl>
 <1524064498394.81978@ufl.edu>,<9345ACEA-864F-484F-BF01-3F287482CE14@wp.pl>
Message-ID: <1524065424968.53087@ufl.edu>

Yeah, that is the problem with UTM coordinates. I do not know a way around it, someone else may know better than me.
Are you sure you need sPCA from such distant areas? Have you already tried PCA? Do you see even a weak clustering? Have you tried DAPC? 

Sorry I can't be more helpful 
Max

Massimiliano S. Tagliamonte
DVM, MSc, PhD
Postdoc Associate
Emerging Pathogens Institute
Department of Pathology
College of Medicine
University of Florida

________________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at <adegenet-forum-bounces at r-forge.wu-wien.ac.at> on behalf of mkonop at wp.pl <mkonop at wp.pl>
Sent: Wednesday, April 18, 2018 11:21 AM
Cc: adegenet-forum at r-forge.wu-wien.ac.at
Subject: Re: [adegenet-forum] Coordinates and distances in sPCA

Dear Massimiliano,
Thanks for quick answer. The problem with UTM and my data is that my samples are in 3 or even 4 UTM zones. I did not find a way to transform such a big area to UTM coordinates.

Maciek

> Wiadomo?? napisana przez Tagliamonte,Massimiliano S <mstagliamonte at ufl.edu> w dniu 18.04.2018, o godz. 17:14:
>
> Dear Maciek,
>
> If I remember correctly, you need to use the UTM coordinate system. I do not have access to my personal computer right now, so you'll have to do some search to find the appropriate conversion programs or packages, it's been some time since I last did it. Feel free to write again if you need any more details.
>
> Regards,
> Max
>
> Massimiliano S. Tagliamonte
> DVM, MSc, PhD
> Postdoc Associate
> Emerging Pathogens Institute
> Department of Pathology
> College of Medicine
> University of Florida
>
> ________________________________________
> From: adegenet-forum-bounces at r-forge.wu-wien.ac.at <adegenet-forum-bounces at r-forge.wu-wien.ac.at> on behalf of Maciek <mkonop at wp.pl>
> Sent: Wednesday, April 18, 2018 11:10 AM
> To: adegenet-forum at r-forge.wu-wien.ac.at
> Subject: [adegenet-forum] Coordinates and distances in sPCA
>
> Dear All,
>
> I've searched tutorials and internet to find what coordinate system
> should be used in sPCA but found no information. I checked data from
> Rupica, but could not figure out what cooridinate system it is. When I
> used regular WGS84 coordinates the distances between points are
> expressed in strange units of approximatelly 78 km but are consistent
> along north/south and east/west distances (however I did not check them
> in detail).
>
> Where should I search for such information?
>
> Cheers,
>
> Maciek
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.r-2Dforge.r-2Dproject.org_cgi-2Dbin_mailman_listinfo_adegenet-2Dforum&d=DwICAg&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=VKMSeIT5HKvjRErWI8R0zntMm_kPWBrZQJU4mlHwsIA&m=3gqPYp35vSvHM-XBpjQ3azNlqgP5MwUR8_2yksZj3oA&s=xUFAx7aTbxmpoRrWI7j4SMwRTpO92DCZuWY_pZdioXg&e=

_______________________________________________
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From thibautjombart at gmail.com  Thu Apr 19 11:59:37 2018
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Thu, 19 Apr 2018 10:59:37 +0100
Subject: [adegenet-forum] different results for pegas and hierfstat Fst
 via weir and cockerham
In-Reply-To: <CANjmwbHieEAoifXLixi_9JRYZ3BQHR7VqFqOp=4S1W3H=ktEmg@mail.gmail.com>
References: <CANjmwbHieEAoifXLixi_9JRYZ3BQHR7VqFqOp=4S1W3H=ktEmg@mail.gmail.com>
Message-ID: <CANPRA+ocbSm8MEYMJJTEKte1_7b7V59prcnz9SpPEwQRkQosRA@mail.gmail.com>

Hi Gary,

it is not the first time we see discrepancies in F stats across different
packages and estimators. As these are related to pegas and hierfstat, maybe
you'll get better feedback posting it as an issue on the github project
pages? I think J?rome and Emmanuel are on the adegenet forum, but they may
miss this.

Best
Thibaut


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

On 13 April 2018 at 00:09, Gary Longo <garycharleslongo at gmail.com> wrote:

> Hi Thibaut and company!
>
> # I've noticed differences with Fst and Fis calculations in Pegas vs
> Hierfstat while using Adegenet
>
> > data("nancycats")
>
> # using weir and cockerham in pegas
> > nancycats_Fstat_as_loci <- Fst(as.loci(nancycats))
> > nancycats_Fstat_as_loci
>
>             Fit        Fst         Fis
> fca8  0.2447420 0.10146648 0.159454807
> fca23 0.1646295 0.06746762 0.104191391
> fca43 0.1514487 0.06893755 0.088620458
> fca45 0.1010807 0.09792456 0.003498722
> fca77 0.2790495 0.10036588 0.198618075
> fca78 0.1842490 0.07025915 0.122603911
> fca90 0.2098744 0.09168833 0.130116240
> fca96 0.2034755 0.10744024 0.107595351
> fca37 0.2604033 0.06985321 0.204860244
>
> # also using weir & cockerham in hierfstat
> > nancycats_hfstat <- genind2hierfstat(nancycats)
> > nancycats_wc <- wc(nancycats_hfstat)
> > nancycats_wc_loci_stats <- as.data.frame(nancycats_wc[["per.loc"]])
> > nancycats_wc_loci_stats
>
>          FST          FIS
> 1 0.10150515  0.148673460
> 2 0.06746762  0.104191391
> 3 0.06893755  0.088620458
> 4 0.07652596 -0.001451681
> 5 0.10036588  0.198618075
> 6 0.07025915  0.122603911
> 7 0.09168833  0.130116240
> 8 0.10981110  0.094857474
> 9 0.06985321  0.204860244
>
>
> > colSums(is.na(nancycats_hfstat))
>
>   pop  fca8 fca23 fca43 fca45 fca77 fca78 fca90 fca96 fca37
>     0    20     0     0    21     0     0     0     9     0
>
>
> The results are identical in loci that are not missing data but are
> different in loci with missing data.
>
> Two questions:
> 1) How are they handling missing data differently since they are both
> using Weir and Cockerham 1984? Follow up: which is better suited for
> calculating Fst and Fis values when there are missing data? I'm analyzing a
> SNP dataset based on ~2100 RADseq loci in over 500 individuals, which of
> course has some missing data at most loci. My results from calculating
> these values in Pegas vs Hierfstat are very different. Specifically Fst and
> Fis values are generally much higher and I don't get any negative Fis
> values when calculated in pegas.
>
> 2) Why does the conversion to hierfstat result in the loss of loci name?
> This would be very useful to retain for downstream comparisons.
>
> Cheers,
> Gary
>
>
> --
> Gary Charles Longo
> NRC Research Associate
> NOAA, National Marine Fisheries Service
> 2725 Montlake Blvd E
> Seattle, WA  98112
> garycharleslongo.wordpress.com
> (831) 247-3056
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/
> listinfo/adegenet-forum
>
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From thibautjombart at gmail.com  Thu Apr 19 13:39:43 2018
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Thu, 19 Apr 2018 12:39:43 +0100
Subject: [adegenet-forum] problem with DAPC/find clusters analyses with
 rad seq data
In-Reply-To: <CALJ95SQw6ddwSSGdh0FZmi7zT3ED-LcSC_u-2zKw2912ZW9QkQ@mail.gmail.com>
References: <CALJ95SQw6ddwSSGdh0FZmi7zT3ED-LcSC_u-2zKw2912ZW9QkQ@mail.gmail.com>
Message-ID: <CANPRA+o4_WQSanwj9rzg+4m5cGBYXPvuwAofVvwOwmtR2yNTAw@mail.gmail.com>

Hello

if your computer can afford it, I would stick to genind objects and use
snapclust. The method is documented there:
tutorial: https://github.com/thibautjombart/adegenet/wiki/Tutorials
podcast: https://www.youtube.com/watch?v=Vl3cf0XHG7Q
paper:
https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12968

Best
Thibaut




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

On 16 April 2018 at 20:00, Lu Maffey <lucia.maffey at gmail.com> wrote:

> Hi Thibaut and everyone!
>
> I need some help with a DAPC analyses I'm trying to perform on my radseq
> data (whole genome for different mosquitoe samples, total of 65
> individuals). (I'm new with Adegenet so I apologize in advance if this
> question is quite basic!). The samples are from different locations and I'm
> trying to stablish if there is population structure within the data. I have
> previously performed analyses using Structure which showed that there are
> different clusters (of course using fewer SNPs than the total number
> available because of the panmixia assumption). So I've created the genlight
> object with all the SNPs(after filtering low frequencies in plink) but when
> I use find.clusters, the BIC against number of clusters graph only shows
> increasing values of BIC. It never decreases. So I know that it's not the
> only way to determine the number of clusters to perform the analysis but
> I'm not sure wether this means that the program doesn't recognize any
> clusters within the data or some other issue. I've tried using the same
> value I've obtained for this data in Structure and it shows a similar
> asignation but I'm not sure if thisis correct.
> If I perform a DAPC analyses, when I use the scatter function to show the
> results, the graph only shows the groups numbers, but no individual dots.
> Could you please give me some insight about what's going on here?
>
> Thank you very much in advance!
>
> cheers
>
> Lu
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/
> listinfo/adegenet-forum
>
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From thibautjombart at gmail.com  Thu Apr 19 16:29:34 2018
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Thu, 19 Apr 2018 15:29:34 +0100
Subject: [adegenet-forum] DAPC- Coloring Points by Source Population,
 but Group Point by Genetic Cluster
In-Reply-To: <CAGcVJpbboetjedTeysTzB+zcsaTmCH31Y=Oi-5qGNgVSaSOMDg@mail.gmail.com>
References: <CAGcVJpbboetjedTeysTzB+zcsaTmCH31Y=Oi-5qGNgVSaSOMDg@mail.gmail.com>
Message-ID: <CANPRA+pr-wAASMyA3-WO8_aeOkcE=11u10PKRqwWoTisDyUUAA@mail.gmail.com>

Hi there

this is not exactly recommended practice, as the color is supposed to
reflect the clustering. If you want to do this, the best way is to make the
plot from scratch using adegraphics:
https://cran.r-project.org/web/packages/adegraphics/vignettes/adegraphics.html

Best
Thibaut


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

On 13 April 2018 at 16:10, Alicia Reigel <reige012 at gmail.com> wrote:

> Hello,
>
> I'm having some trouble working through an issue in DAPC. I've been using
> scatter and DAPC to plot my points from microsatellite data. I have
> definitely figured out how to cluster and color the points for the
> individuals by their genetic cluster and by their original populations, but
> what I can't determine is how to color each point by the original source
> population, but cluster them by their genetic cluster.  Can anyone help me
> with this?
>
> Thanks,
> Alicia Reigel
>
> --
> Ph.D. Candidate, Louisiana State University | Michael E.Hellberg Lab
> M.S. Biology, Georgia Southern University | Daniel F. Gleason Lab
> Lab Phone: (225) 578-9114
> Email: areige1 at lsu.edu
> Website: aliciamreigel.wordpress.com
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/
> listinfo/adegenet-forum
>
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From amaranta.fontcuberta at gmail.com  Fri Apr 20 14:50:46 2018
From: amaranta.fontcuberta at gmail.com (Amaranta)
Date: Fri, 20 Apr 2018 14:50:46 +0200
Subject: [adegenet-forum] selecting SNPs according to chromosome list
Message-ID: <CAG+96r-j0SFbR4rJfQ46LqcoH++tPmafpfWrU=Rjvg-WGiyC5g@mail.gmail.com>

Hello,

I am working with a genelight object. I would like to do analsyes on a
subset of SNPs, defined by a list of chromosomes.  Is there a way to do
this in adegenet ?
 I know I could convert the genelight object to a matrix and select columns
according to a list of names. But I am interested in keeping the
information of the genelight object.  Also, I know there is the Seploc()
function that subsets the dataset in groups of /random/ SNPs. Is there way
to use Seploc() to select locus according to a criteria?

Many thanks in advance,


Amaranta.
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From thibautjombart at gmail.com  Fri Apr 20 18:04:44 2018
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Fri, 20 Apr 2018 17:04:44 +0100
Subject: [adegenet-forum] selecting SNPs according to chromosome list
In-Reply-To: <CAG+96r-j0SFbR4rJfQ46LqcoH++tPmafpfWrU=Rjvg-WGiyC5g@mail.gmail.com>
References: <CAG+96r-j0SFbR4rJfQ46LqcoH++tPmafpfWrU=Rjvg-WGiyC5g@mail.gmail.com>
Message-ID: <CANPRA+pLRhFCd7JLSbsYJoQTHYRdop_pidOH9N9HuJQ1kLOQFA@mail.gmail.com>

Hello,

here's an example using made up data:

## make up data
> x <- glSim(40, 1e4, LD=FALSE, parallel=FALSE)

## fake chromosome info
> chromosome(x) <- rep(c("chr1", "chr2"), c(2000, 8000))

## create a list of genlights, 1 per chromosome
> lapply(levels(chromosome(x)), function(lev) x[,chromosome(x)==lev])
[[1]]
 /// GENLIGHT OBJECT /////////

 // 40 genotypes,  2,000 binary SNPs, size: 73.5 Kb
 0 (0 %) missing data

 // Basic content
   @gen: list of 40 SNPbin
   @ploidy: ploidy of each individual  (range: 1-1)

 // Optional content
   @chromosome: factor storing chromosomes of the SNPs
   @other: a list containing: ancestral.pops


[[2]]
 /// GENLIGHT OBJECT /////////

 // 40 genotypes,  8,000 binary SNPs, size: 126.3 Kb
 0 (0 %) missing data

 // Basic content
   @gen: list of 40 SNPbin
   @ploidy: ploidy of each individual  (range: 1-1)

 // Optional content
   @chromosome: factor storing chromosomes of the SNPs
   @other: a list containing: ancestral.pops


This could be an option in seploc; I don't really have time to implement it
now but maybe worth filing as an issue on github?

Note that if you want to randomise SNPs you can tweak the above using
'sample'.
Best
Thibaut



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

On 20 April 2018 at 13:50, Amaranta <amaranta.fontcuberta at gmail.com> wrote:

> Hello,
>
> I am working with a genelight object. I would like to do analsyes on a
> subset of SNPs, defined by a list of chromosomes.  Is there a way to do
> this in adegenet ?
>  I know I could convert the genelight object to a matrix and select
> columns according to a list of names. But I am interested in keeping the
> information of the genelight object.  Also, I know there is the Seploc()
> function that subsets the dataset in groups of /random/ SNPs. Is there way
> to use Seploc() to select locus according to a criteria?
>
> Many thanks in advance,
>
>
> Amaranta.
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/
> listinfo/adegenet-forum
>
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From handalwilliam2 at gmail.com  Wed Apr 25 15:43:23 2018
From: handalwilliam2 at gmail.com (William Handal)
Date: Wed, 25 Apr 2018 15:43:23 +0200
Subject: [adegenet-forum] Genpop object-weak structure
Message-ID: <CAJjMGzYiy6mM8fihtrqTbE5uZ-YdPbVHQZUFaid8bZC1B4JGug@mail.gmail.com>

Dear adegenet commnunity,

I am working with microsatellites and I am studying weak genetic structure
population.
When I perform multivariate anaysis with genind, or genpop object no
structure is observed.

When I perform RDA with genind object and coordinates as explanatory
variable no significant
results appear.

However when I perform RDA with genpop object and coordinates as
explanatory variable significant results appear, with Rsquaredadjust of
17%.Therefore melting individuals by sample influence the RDA results.

Is it ok if I perform RDA anaylsis on genpop object, or do I introduce a
bias?

Many thanks to all of you,

Best regards,

William
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From tirupathiraobt at gmail.com  Thu Apr 26 02:51:29 2018
From: tirupathiraobt at gmail.com (thiru rao)
Date: Thu, 26 Apr 2018 06:21:29 +0530
Subject: [adegenet-forum] Fwd: Monmonier's algorithm in Adegenet
In-Reply-To: <CALe2N_szx79dRMDoOW01MvGTQv9emVPg1jg7v6-xg6N1bJxRkQ@mail.gmail.com>
References: <CALe2N_szx79dRMDoOW01MvGTQv9emVPg1jg7v6-xg6N1bJxRkQ@mail.gmail.com>
Message-ID: <CALe2N_tZRaJVR1dgBeMyf6VzoZJ+PWQhDwJSF9EZB2hMVpQcMA@mail.gmail.com>

Hi Everyone,

I'd like to useMomonier's algorithm in adegenet. I've generated SNPs data
from marine fish, would like to use population distance. Can you please
suggest what kind of file I can use it?

Kind regards,
Tiru



-- 
Best regards

G.Tirupathi Rao,
Senior Research Fellow,
Centre For Cellular and Molecular Biology(CCMB),
Hyderabad,India.
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From thibautjombart at gmail.com  Thu Apr 26 12:54:32 2018
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Thu, 26 Apr 2018 11:54:32 +0100
Subject: [adegenet-forum] Fwd: Monmonier's algorithm in Adegenet
In-Reply-To: <CALe2N_tZRaJVR1dgBeMyf6VzoZJ+PWQhDwJSF9EZB2hMVpQcMA@mail.gmail.com>
References: <CALe2N_szx79dRMDoOW01MvGTQv9emVPg1jg7v6-xg6N1bJxRkQ@mail.gmail.com>
 <CALe2N_tZRaJVR1dgBeMyf6VzoZJ+PWQhDwJSF9EZB2hMVpQcMA@mail.gmail.com>
Message-ID: <CANPRA+pnU9HAhNTxVrcKHybHfVkNAO9HZ7Jpr1PWz6xerkBiVg@mail.gmail.com>

Hi there

Imports of data and Monmonier are all documented in the basics tutorial:
https://github.com/thibautjombart/adegenet/wiki/Tutorials

Cheers
Thibaut


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

On 26 April 2018 at 01:51, thiru rao <tirupathiraobt at gmail.com> wrote:

>
> Hi Everyone,
>
> I'd like to useMomonier's algorithm in adegenet. I've generated SNPs data
> from marine fish, would like to use population distance. Can you please
> suggest what kind of file I can use it?
>
> Kind regards,
> Tiru
>
>
>
> --
> Best regards
>
> G.Tirupathi Rao,
> Senior Research Fellow,
> Centre For Cellular and Molecular Biology(CCMB),
> Hyderabad,India.
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/
> listinfo/adegenet-forum
>
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