From thibautjombart at gmail.com  Mon Jan  2 17:04:30 2017
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Mon, 2 Jan 2017 16:04:30 +0000
Subject: [adegenet-forum] tetraploid DAPC
In-Reply-To: <CA+OwOyVM_scL6E-K7S7U3ao6h367Q69gHV_TxVj-tWFRE0MCCg@mail.gmail.com>
References: <CA+OwOyVM_scL6E-K7S7U3ao6h367Q69gHV_TxVj-tWFRE0MCCg@mail.gmail.com>
Message-ID: <CANPRA+pBT2dBu4KDqRiRXgXAu664CnKQE0WuU=jkTZqVUecVfg@mail.gmail.com>

Dear Jessica,

as you might have noted from the doc of read.structure, the function only
work with diploid data. Tetraploid data are no problem in adegenet, but
you'll need to get them in differently. I would suggest the following
workflow:

1) get your data in a txt/csv file in a format where data at each locus are
coded as character strings where alleles are separated by a given symbol
(e.g. "-", or "/")
001-010-001-002

2) read them into R using read.table or read.csv

3) use df2genind to convert data into a genind object

The basics tutorial should help with this last step:
https://github.com/thibautjombart/adegenet/wiki/Tutorials

Best
Thibaut


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

On 30 November 2016 at 13:28, Jessica Perez Alquicira <
perezalquicira at gmail.com> wrote:

> Hi, I would like to do a dapc on tetraploid data. My file format is in
> structure.
> I have not find this information in the manual. Could you please let me
> know how could I do that.
>
> Best
>
> _______________________________________________
> 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 Jan  2 16:59:59 2017
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Mon, 2 Jan 2017 15:59:59 +0000
Subject: [adegenet-forum] Difference in assignment between versions of
 adegenet (DAPC)
In-Reply-To: <7D7675C38641E241926881C240902CDA0C1E9C49@ait-pex02mbx05.win.dtu.dk>
References: <7D7675C38641E241926881C240902CDA0C1E9C49@ait-pex02mbx05.win.dtu.dk>
Message-ID: <CANPRA+p9vNkQG7+fa-0agHoR-JB9nruyaPwN-iSsRs=aFWHhzA@mail.gmail.com>

Dear Ole and Team,

sorry, this message was stuck in the moderation limbos for a while. Best
subscribe to skip this.

There's been a bunch of changes since the older version, but the main one I
can think of in this case is that a bug has been fixed in predict.dapc when
supplementary individuals are used. In some versions prior to 2.0, data
were not scaled before being projected onto the discriminant functions,
resulting in some erroneous predictions. In practice, it seems
supplementary individuals tended to be too drastically assigned to a given
group, though not too wrongly (in the microbov example predictions still
made sense). This said, I'm not aware of any systematic study of the issue.

At any rate, trust the current version.

Best
Thibaut


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

On 14 December 2016 at 14:05, Ole Henriksen <ohen at aqua.dtu.dk> wrote:

> Hi Thibaut and Co
>
>
>
> We're a team who have used *adegenet*'s (version *1-4.1 *and *1-4.2 *) DAPC
> assignment method for some earlier studies. We are now encountering
> problems using the assignment method. The problem is that the new version *adegenet
> 2.0.1 *assigns "old individuals", which we have used in earlier studies, differently
> compared to assignments with earlier versions of the package.
>
>
>
> We use SNP data, and our gen-files look as shown below. Alleles are coded
> by three digits. Se example below
>
> ______________________________________________
>
> GenePop file, with 5 samples & 96 loci
>
> cgpGmo-S1017
>
> cgpGmo-S1018a
>
> cgpGmo-S1026
>
> cgpGmo-S1070
>
> cgpGmo-S1095
>
> cgpGmo-S1103
>
> POP
>
> DAB08_01 , 001001 002002 001002 002001 001001 001001
>
> DAB08_02 , 001001 002002 001001 002002 001001 002002
>
> DAB08_03 , 001001 002002 001001 002002 001001 002001
>
> POP
>
> INC02_01 , 001001 002002 001002 002002 001001 002001
>
> INC02_02 , 001001 002002 002002 002002 001001 002002
>
> INC02_03 , 001001 002002 001002 002002 001001 002001
>
> __________________________________________
>
>
>
> We have two issues
>
>
>
> 1) Last year we assigned individuals using version *adegenet 1-4.1.*We
> suspected that is must be something with how the file are read, and we
> wanted to check and compare with older versions (*1-4.1 *and *1-4.2*).
> We've tried to use older versions with *install_version()* to make the
> comparison between versions (*1-4.1*, *1-4.2 *and *2.0.1*), but we keep
> getting following error message when using older versions.
>
> ___________________________________________
>
> * Converting data from a Genepop .gen file to a genind object... *
>
>
>
>
>
> *File description:  GenePop file, with 5 samples & 96 loci *
>
> *Error in while (keepCheck) { : missing value where TRUE/FALSE needed*
>
> *____________________________________________________________*
>
>
>
> We do not understand why we get this error message, when we use the exact
> same files as we have always used. Any idea?
>
>
>
> 2) When we use the newest version, we get a different assignment result compared
> to assignments with earlier versions of the package.
>
> I have my previous assignment results for assigned individuals (*1-4.1 *
> and *1-4.2*). I reassigned these individuals with the new package (*2.0.1*).
> Thereafter, I've compared the assignment between package versions and they
> are different, even though we retain the same number of PC's, use same
> reference file and use the same script with some minor corrections for
> reading files to accommodate the new version. Any idea why this is the
> case? Any changes to how each locus and allele are read from version to
> version?
>
>
>
> I have noticed that there is a difference between assignment when using
> adegenet (*2.0.1*)  depending on the individuals I include in a gen-file
> for assignment. When I assign all my individuals from all years in one
> file, it will give a different assignment result than when I assign single
> files where they are divided up into years.
>
> Can it be the positioning of alleles at each locus which have changed? We
> are not sure what is going wrong, but we suspect that it is something with
> the reading of our files.
>
>
>
> Below is some R-history, which hopefully. might be helpful
>
> R-script:
>
> ______________________________________________
>
> #Reading files
>
> Ref <- read.genepop("Ref.gen", ncode = 3)
>
> Assign <- read.genepop("TBA_All.gen", ncode = 3)
>
> #DAPC
>
> DAPC_Ref<-dapc(Ref, pop(Ref), n.pca=100, n.da=3)
>
> #Assignment
>
> Predict=predict.dapc(DAPC_Ref, newdata=Assign)
>
> Predict$assign
>
>
>
> Genind objects after *read.genepop()*:
>
> ___________________________________
>
> >Reference
>
> /// GENIND OBJECT /////////
>
>
>
>  // 487 individuals; 96 loci; 192 alleles; size: 451.5 Kb
>
>
>
>  // Basic content
>
>    @tab:  487 x 192 matrix of allele counts
>
>    @loc.n.all: number of alleles per locus (range: 2-2)
>
>    @loc.fac: locus factor for the 192 columns of @tab
>
>    @all.names: list of allele names for each locus
>
>    @ploidy: ploidy of each individual  (range: 2-2)
>
>    @type:  codom
>
>    @call: read.genepop(file = "Ref.gen", ncode = 3)
>
>
>
>  // Optional content
>
>    @pop: population of each individual (group size range: 62-215)
>
>
>
> >AssignAll #All individuals for all years
>
> /// GENIND OBJECT /////////
>
>
>
>  // 1,357 individuals; 96 loci; 192 alleles; size: 1.1 Mb
>
>
>
>  // Basic content
>
>    @tab:  1357 x 192 matrix of allele counts
>
>    @loc.n.all: number of alleles per locus (range: 2-2)
>
>    @loc.fac: locus factor for the 192 columns of @tab
>
>    @all.names: list of allele names for each locus
>
>    @ploidy: ploidy of each individual  (range: 2-2)
>
>    @type:  codom
>
>    @call: read.genepop(file = "TBA_All.gen", ncode = 3)
>
>
>
>  // Optional content
>
>    @pop: population of each individual (group size range: 1357-1357)
>
>
>
> > Assign2015 #individuals for year 2015 only
>
> /// GENIND OBJECT /////////
>
>
>
>  // 469 individuals; 96 loci; 192 alleles; size: 434.2 Kb
>
>
>
>  // Basic content
>
>    @tab:  469 x 192 matrix of allele counts
>
>    @loc.n.all: number of alleles per locus (range: 2-2)
>
>    @loc.fac: locus factor for the 192 columns of @tab
>
>    @all.names: list of allele names for each locus
>
>    @ploidy: ploidy of each individual  (range: 2-2)
>
>    @type:  codom
>
>    @call: read.genepop(file = "TBA_Fisk2015.gen", ncode = 3)
>
>
>
>  // Optional content
>
>    @pop: population of each individual (group size range: 469-469)
>
>
>
> Assignment result showing different assignment depending on which
> individuals one include in a input-file (gen-file) for assignment is after
> *predict.dapc()*:
>
> _______________________________________________________
>
> > Predict$assign #All individuals for all years
>
>    [1] TAS10_30 TAS10_30 TAS10_30 TAS10_30 UMM45_39 UMM45_39
>
>    [7] UMM45_39 UMM45_39 TAS10_30 TAS10_30 UMM45_39 UMM45_39
>
>   [13] ISC02_39 UMM45_39 ISC02_39 ISC02_39 ISC02_39 ISC02_39
>
>   [19] UMM45_39 QOR08_30 ISC02_39 UMM45_39 TAS10_30 UMM45_39
>
>   [25] QOR08_30 QOR08_30 UMM45_39 QOR08_30 QOR08_30 UMM45_39
>
>   [31] UMM45_39 UMM45_39 QOR08_30 UMM45_39 UMM45_39 ISC02_39
>
>   [37] ISC02_39 UMM45_39 UMM45_39 QOR08_30 UMM45_39 QOR08_30
>
>   [43] UMM45_39 UMM45_39 UMM45_39 UMM45_39 QOR08_30 UMM45_39
>
>                              etc.
>
>
>
> > Predict$assign #individuals for year 2015 only
>
>   [1] TAS10_30 TAS10_30 TAS10_30 TAS10_30 TAS10_30 TAS10_30
>
>   [7] TAS10_30 TAS10_30 TAS10_30 TAS10_30 UMM45_39 UMM45_39
>
>  [13] UMM45_39 UMM45_39 UMM45_39 UMM45_39 UMM45_39 UMM45_39
>
>  [19] UMM45_39 UMM45_39 ISC02_39 ISC02_39 ISC02_39 ISC02_39
>
>  [25] ISC02_39 ISC02_39 TAS10_30 ISC02_39 ISC02_39 ISC02_39
>
>  [31] ISC02_39 ISC02_39 ISC02_39 ISC02_39 ISC02_39 TAS10_30
>
>  [37] ISC02_39 ISC02_39 ISC02_39 ISC02_39 ISC02_39 TAS10_30
>
>  [43] ISC02_39 ISC02_39 ISC02_39 ISC02_39 ISC02_39 ISC02_39
>
>                              etc.
>
>
>
> Thank you
>
> Sincerely
>
> Ole and team
>
>
>
> _______________________________________________
> 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 perezalquicira at gmail.com  Tue Jan  3 18:02:04 2017
From: perezalquicira at gmail.com (Jessica Perez Alquicira)
Date: Tue, 3 Jan 2017 11:02:04 -0600
Subject: [adegenet-forum] tetraploid DAPC
In-Reply-To: <CANPRA+pBT2dBu4KDqRiRXgXAu664CnKQE0WuU=jkTZqVUecVfg@mail.gmail.com>
References: <CA+OwOyVM_scL6E-K7S7U3ao6h367Q69gHV_TxVj-tWFRE0MCCg@mail.gmail.com>
 <CANPRA+pBT2dBu4KDqRiRXgXAu664CnKQE0WuU=jkTZqVUecVfg@mail.gmail.com>
Message-ID: <CA+OwOyVGwOzgUvYK9ErA5VvsuKfwfGFNt91QovnYHc_Na-ia=A@mail.gmail.com>

Dear Thibaut, I have this file format (including 149 samples, pop number, 8
loci with four alleles)
Buen137,1,04/07/04/07,11/13/11/13,05/07/05/07,06/19/21/06,
05/06/05/06,03/03/03/03,03/05/03/05,07/07/07/07

I am doing the following things:
obj<-read.csv("testCSV.csv",header=FALSE)
obj2 <- df2genind(obj, sep = "/", ind.names = TRUE, loc.names = FALSE, pop
= TRUE, ploidy = 4, type = c("codom"))

And I am getting this error:
Error in `rownames<-`(`*tmp*`, value = "TRUE") :
  length of 'dimnames' [1] not equal to array extent

Not sure what to do, any help?
Thanks so much for your support


2017-01-02 10:04 GMT-06:00 Thibaut Jombart <thibautjombart at gmail.com>:

> Dear Jessica,
>
> as you might have noted from the doc of read.structure, the function only
> work with diploid data. Tetraploid data are no problem in adegenet, but
> you'll need to get them in differently. I would suggest the following
> workflow:
>
> 1) get your data in a txt/csv file in a format where data at each locus
> are coded as character strings where alleles are separated by a given
> symbol (e.g. "-", or "/")
> 001-010-001-002
>
> 2) read them into R using read.table or read.csv
>
> 3) use df2genind to convert data into a genind object
>
> The basics tutorial should help with this last step:
> https://github.com/thibautjombart/adegenet/wiki/Tutorials
>
> Best
> Thibaut
>
>
> --
> Dr Thibaut Jombart
> Lecturer, Department of Infectious Disease Epidemiology, Imperial College
> London
> Head of RECON: repidemicsconsortium.org
> sites.google.com/site/thibautjombart/
> github.com/thibautjombart
> Twitter: @TeebzR <http://twitter.com/TeebzR>
> +44(0)20 7594 3658
>
> On 30 November 2016 at 13:28, Jessica Perez Alquicira <
> perezalquicira at gmail.com> wrote:
>
>> Hi, I would like to do a dapc on tetraploid data. My file format is in
>> structure.
>> I have not find this information in the manual. Could you please let me
>> know how could I do that.
>>
>> Best
>>
>> _______________________________________________
>> 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 mstagliamonte at ufl.edu  Tue Jan  3 22:03:02 2017
From: mstagliamonte at ufl.edu (Tagliamonte,Massimiliano S)
Date: Tue, 3 Jan 2017 21:03:02 +0000
Subject: [adegenet-forum] df2genind function unexpected behavior
Message-ID: <1483477381184.77044@ufl.edu>

Dear Dr. Jombart,


I am currently trying to perform a sPCA, and I have noticed something unexpected while formatting my datasets.

I have used the function df2genind, then tried to add the spatial data using the command:


my_genind_obj$other$xy<- my_dataframe[,c('X','Y')]  #X and Y are the utm coordinate columns;


When checking that the data were imported correctly though, I realized that the coordinates were sorted in the same order than the original dataframe; the isolates themselves though (my_genind_obj$table) were sorted in some other way (it seemed alphanumerical, but isolate names starting with "X" were put before the ones starting with "P"). I guess this breaks the correlation between each isolate and its location. My isolate names are aplhanumeric, and the names starting with "X" also contain dots (e.g. "X.14.4.555)". Am I missing something? Is there a better way to attach the spatial information so to keep correlation between different pieces of information?

I am using adegenet v.2.0.1 on Windows 7.

Thank you for your kind attention,


Massimiliano S. Tagliamonte
Graduate Student
University of Florida
College of Veterinary Medicine
Department of Infectious Diseases and Pathology
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From mstagliamonte at ufl.edu  Tue Jan  3 22:36:20 2017
From: mstagliamonte at ufl.edu (Tagliamonte,Massimiliano S)
Date: Tue, 3 Jan 2017 21:36:20 +0000
Subject: [adegenet-forum] df2genind function unexpected behavior
In-Reply-To: <1483477381184.77044@ufl.edu>
References: <1483477381184.77044@ufl.edu>
Message-ID: <1483479380905.26272@ufl.edu>

Update:

OK, I have replaced the dots (".") in the names with "_", now the order of the isolates is maintained. I'll have to keep in mind this behavior. I guess it's a bad idea to introduce special characters in my data in R.


Sincerely,


Massimiliano S. Tagliamonte
Graduate Student
University of Florida
College of Veterinary Medicine
Department of Infectious Diseases and Pathology

________________________________
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From roman.lustrik at biolitika.si  Tue Jan  3 23:44:41 2017
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Tue, 3 Jan 2017 23:44:41 +0100 (CET)
Subject: [adegenet-forum] df2genind function unexpected behavior
In-Reply-To: <1483479380905.26272@ufl.edu>
References: <1483477381184.77044@ufl.edu> <1483479380905.26272@ufl.edu>
Message-ID: <672841075.230621.1483483481140.JavaMail.zimbra@biolitika.si>

Can you provide a reproducible example? 

FWIW, you can use accessor functions like `tab(genind_obj)` or access the other slot through `other(genind_obj)`, e.g. 

library(adegenet) 

data(nancycats) 

other(nancycats)$xy 

or assigning things 

other(nancycats)$xy <- xy_object 

To access genotypes, you can use 

tab(nancycats) 


Cheers, 
Roman 

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


From: "Tagliamonte,Massimiliano S" <mstagliamonte at ufl.edu> 
To: "adegenet-forum at lists.r-forge.r-project.org" <adegenet-forum at r-forge.wu-wien.ac.at> 
Sent: Tuesday, January 3, 2017 10:36:20 PM 
Subject: Re: [adegenet-forum] df2genind function unexpected behavior 



Update: 

OK, I have replaced the dots (".") in the names with "_", now the order of the isolates is maintained. I'll have to keep in mind this behavior. I guess it's a bad idea to introduce special characters in my data in R. 




Sincerely, 


Massimiliano S. Tagliamonte 
Graduate Student 
University of Florida 
College of Veterinary Medicine 
Department of Infectious Diseases and Pathology 



_______________________________________________ 
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  Tue Jan  3 23:52:37 2017
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Tue, 3 Jan 2017 23:52:37 +0100 (CET)
Subject: [adegenet-forum] tetraploid DAPC
In-Reply-To: <CA+OwOyVGwOzgUvYK9ErA5VvsuKfwfGFNt91QovnYHc_Na-ia=A@mail.gmail.com>
References: <CA+OwOyVM_scL6E-K7S7U3ao6h367Q69gHV_TxVj-tWFRE0MCCg@mail.gmail.com>
 <CANPRA+pBT2dBu4KDqRiRXgXAu664CnKQE0WuU=jkTZqVUecVfg@mail.gmail.com>
 <CA+OwOyVGwOzgUvYK9ErA5VvsuKfwfGFNt91QovnYHc_Na-ia=A@mail.gmail.com>
Message-ID: <1451329397.230666.1483483957430.JavaMail.zimbra@biolitika.si>

Hi Jessica, 

you forgot to exclude the columns not responsible for forming genotypes. Also, you misunderstood how ind.names and loc.names work. If not NULL, you should provide the arguments with vectors. 

library(adegenet) 

x <- "Buen137,1,04/07/04/07,11/13/11/13,05/07/05/07,06/19/21/06,05/06/05/06,03/03/03/03,03/05/03/05,07/07/07/07" 

xy <- read.table(text = x, sep = ",") 

df2genind(X = xy[, c(-1, -2)], sep = "/", ploidy = 4) 

If you want for ind.names to work out of the box, you could remove the columns for names and place it as a rownames, like so: 

rownames(xy) <- xy[, 1] 
xy[, 1] <- NULL 

df2genind(X = xy[, -2], sep = "/", ploidy = 4) 

Cheers, 
Roman 

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


From: "Jessica Perez Alquicira" <perezalquicira at gmail.com> 
To: "Thibaut Jombart" <thibautjombart at gmail.com> 
Cc: adegenet-forum at lists.r-forge.r-project.org 
Sent: Tuesday, January 3, 2017 6:02:04 PM 
Subject: Re: [adegenet-forum] tetraploid DAPC 

Dear Thibaut, I have this file format (including 149 samples, pop number, 8 loci with four alleles) 
Buen137,1,04/07/04/07,11/13/11/13,05/07/05/07,06/19/21/06,05/06/05/06,03/03/03/03,03/05/03/05,07/07/07/07 

I am doing the following things: 
obj<-read.csv("testCSV.csv",header=FALSE) 
obj2 <- df2genind(obj, sep = "/", ind.names = TRUE, loc.names = FALSE, pop = TRUE, ploidy = 4, type = c("codom")) 

And I am getting this error: 
Error in `rownames<-`(`*tmp*`, value = "TRUE") : 
length of 'dimnames' [1] not equal to array extent 

Not sure what to do, any help? 
Thanks so much for your support 


2017-01-02 10:04 GMT-06:00 Thibaut Jombart < thibautjombart at gmail.com > : 



Dear Jessica, 
as you might have noted from the doc of read.structure, the function only work with diploid data. Tetraploid data are no problem in adegenet, but you'll need to get them in differently. I would suggest the following workflow: 

1) get your data in a txt/csv file in a format where data at each locus are coded as character strings where alleles are separated by a given symbol (e.g. "-", or "/") 
001-010-001-002 

2) read them into R using read.table or read.csv 

3) use df2genind to convert data into a genind object 

The basics tutorial should help with this last step: 
https://github.com/thibautjombart/adegenet/wiki/Tutorials 

Best 
Thibaut 


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

On 30 November 2016 at 13:28, Jessica Perez Alquicira < perezalquicira at gmail.com > wrote: 

BQ_BEGIN

Hi, I would like to do a dapc on tetraploid data. My file format is in structure. 
I have not find this information in the manual. Could you please let me know how could I do that. 

Best 

_______________________________________________ 
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 





BQ_END



_______________________________________________ 
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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  Tue Jan  3 23:54:44 2017
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Tue, 3 Jan 2017 23:54:44 +0100 (CET)
Subject: [adegenet-forum] tetraploid DAPC
In-Reply-To: <1451329397.230666.1483483957430.JavaMail.zimbra@biolitika.si>
References: <CA+OwOyVM_scL6E-K7S7U3ao6h367Q69gHV_TxVj-tWFRE0MCCg@mail.gmail.com>
 <CANPRA+pBT2dBu4KDqRiRXgXAu664CnKQE0WuU=jkTZqVUecVfg@mail.gmail.com>
 <CA+OwOyVGwOzgUvYK9ErA5VvsuKfwfGFNt91QovnYHc_Na-ia=A@mail.gmail.com>
 <1451329397.230666.1483483957430.JavaMail.zimbra@biolitika.si>
Message-ID: <844119247.230684.1483484084239.JavaMail.zimbra@biolitika.si>

Just realized there was a mistake in the last line of my code. Since we remove the sample name from as the first column, the second column becomes first. This is the bane of working with indices and not column names (where things can be handles in a more general manner). In any case, this is the correct line: 

df2genind(X = xy[, -1], sep = "/", ploidy = 4) 

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


From: "Roman Lu?trik" <roman.lustrik at biolitika.si> 
To: "Jessica Perez Alquicira" <perezalquicira at gmail.com> 
Cc: "Thibaut Jombart" <thibautjombart at gmail.com>, adegenet-forum at lists.r-forge.r-project.org 
Sent: Tuesday, January 3, 2017 11:52:37 PM 
Subject: Re: [adegenet-forum] tetraploid DAPC 

Hi Jessica, 

you forgot to exclude the columns not responsible for forming genotypes. Also, you misunderstood how ind.names and loc.names work. If not NULL, you should provide the arguments with vectors. 

library(adegenet) 

x <- "Buen137,1,04/07/04/07,11/13/11/13,05/07/05/07,06/19/21/06,05/06/05/06,03/03/03/03,03/05/03/05,07/07/07/07" 

xy <- read.table(text = x, sep = ",") 

df2genind(X = xy[, c(-1, -2)], sep = "/", ploidy = 4) 

If you want for ind.names to work out of the box, you could remove the columns for names and place it as a rownames, like so: 

rownames(xy) <- xy[, 1] 
xy[, 1] <- NULL 

df2genind(X = xy[, -2], sep = "/", ploidy = 4) 

Cheers, 
Roman 

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


From: "Jessica Perez Alquicira" <perezalquicira at gmail.com> 
To: "Thibaut Jombart" <thibautjombart at gmail.com> 
Cc: adegenet-forum at lists.r-forge.r-project.org 
Sent: Tuesday, January 3, 2017 6:02:04 PM 
Subject: Re: [adegenet-forum] tetraploid DAPC 

Dear Thibaut, I have this file format (including 149 samples, pop number, 8 loci with four alleles) 
Buen137,1,04/07/04/07,11/13/11/13,05/07/05/07,06/19/21/06,05/06/05/06,03/03/03/03,03/05/03/05,07/07/07/07 

I am doing the following things: 
obj<-read.csv("testCSV.csv",header=FALSE) 
obj2 <- df2genind(obj, sep = "/", ind.names = TRUE, loc.names = FALSE, pop = TRUE, ploidy = 4, type = c("codom")) 

And I am getting this error: 
Error in `rownames<-`(`*tmp*`, value = "TRUE") : 
length of 'dimnames' [1] not equal to array extent 

Not sure what to do, any help? 
Thanks so much for your support 


2017-01-02 10:04 GMT-06:00 Thibaut Jombart < thibautjombart at gmail.com > : 



Dear Jessica, 
as you might have noted from the doc of read.structure, the function only work with diploid data. Tetraploid data are no problem in adegenet, but you'll need to get them in differently. I would suggest the following workflow: 

1) get your data in a txt/csv file in a format where data at each locus are coded as character strings where alleles are separated by a given symbol (e.g. "-", or "/") 
001-010-001-002 

2) read them into R using read.table or read.csv 

3) use df2genind to convert data into a genind object 

The basics tutorial should help with this last step: 
https://github.com/thibautjombart/adegenet/wiki/Tutorials 

Best 
Thibaut 


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

On 30 November 2016 at 13:28, Jessica Perez Alquicira < perezalquicira at gmail.com > wrote: 

BQ_BEGIN

Hi, I would like to do a dapc on tetraploid data. My file format is in structure. 
I have not find this information in the manual. Could you please let me know how could I do that. 

Best 

_______________________________________________ 
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 





BQ_END



_______________________________________________ 
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 mstagliamonte at ufl.edu  Wed Jan  4 16:05:03 2017
From: mstagliamonte at ufl.edu (Tagliamonte,Massimiliano S)
Date: Wed, 4 Jan 2017 15:05:03 +0000
Subject: [adegenet-forum] df2genind function unexpected behavior
In-Reply-To: <672841075.230621.1483483481140.JavaMail.zimbra@biolitika.si>
References: <1483477381184.77044@ufl.edu> <1483479380905.26272@ufl.edu>,
 <672841075.230621.1483483481140.JavaMail.zimbra@biolitika.si>
Message-ID: <1483542303096.59786@ufl.edu>

Thank you for your help, Roman,


By asking me to provide an example you made me realize something. I tried again this morning, with exactly the same commands, and could not reproduce  the issue. This is weird. It is not the first time it happens though, i.e. getting unexpected behavior in R which I could not replicate after rebooting. I have no idea what the cause could be. Some of the packages I had loaded yesterday (apart from Adegenet) were not loaded today. I guess I'll have to be even more paranoid and check that each step of my analysis does what is supposed to be doing.


Cheers,

Max


Massimiliano S. Tagliamonte
Graduate Student
University of Florida
College of Veterinary Medicine
Department of Infectious Diseases and Pathology
________________________________
From: Roman Lu?trik <roman.lustrik at biolitika.si>
Sent: Tuesday, January 3, 2017 5:44 PM
To: Tagliamonte,Massimiliano S
Cc: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] df2genind function unexpected behavior

Can you provide a reproducible example?

FWIW, you can use accessor functions like `tab(genind_obj)` or access the other slot through `other(genind_obj)`, e.g.

library(adegenet)

data(nancycats)

other(nancycats)$xy

or assigning things

other(nancycats)$xy <- xy_object

To access genotypes, you can use

tab(nancycats)


Cheers,
Roman

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

________________________________
From: "Tagliamonte,Massimiliano S" <mstagliamonte at ufl.edu>
To: "adegenet-forum at lists.r-forge.r-project.org" <adegenet-forum at r-forge.wu-wien.ac.at>
Sent: Tuesday, January 3, 2017 10:36:20 PM
Subject: Re: [adegenet-forum] df2genind function unexpected behavior


Update:

OK, I have replaced the dots (".") in the names with "_", now the order of the isolates is maintained. I'll have to keep in mind this behavior. I guess it's a bad idea to introduce special characters in my data in R.


Sincerely,


Massimiliano S. Tagliamonte
Graduate Student
University of Florida
College of Veterinary Medicine
Department of Infectious Diseases and Pathology

________________________________

_______________________________________________
adegenet-forum mailing list
adegenet-forum at lists.r-forge.r-project.org
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From vojta at trapa.cz  Wed Jan  4 16:17:19 2017
From: vojta at trapa.cz (=?utf-8?B?Vm9qdMSbY2g=?= Zeisek)
Date: Wed, 04 Jan 2017 16:17:19 +0100
Subject: [adegenet-forum] df2genind function unexpected behavior
In-Reply-To: <1483542303096.59786@ufl.edu>
References: <1483477381184.77044@ufl.edu>
 <672841075.230621.1483483481140.JavaMail.zimbra@biolitika.si>
 <1483542303096.59786@ufl.edu>
Message-ID: <1922273.q79CFg48Aa@tilia>

Hello,
if You load new library and it by coincidence contain a function with same 
name as one of the already loaded functions, the old one is replaced by the 
new one. When loading such library, the R says which functions are replaced. 
This can be common source of problems. Check it.
Sincerely,
V.

Dne st?eda 4. ledna 2017 15:05:03 CET, Tagliamonte,Massimiliano S napsal(a):
> Thank you for your help, Roman,
> 
> By asking me to provide an example you made me realize something. I tried
> again this morning, with exactly the same commands, and could not reproduce
>  the issue. This is weird. It is not the first time it happens though, i.e.
> getting unexpected behavior in R which I could not replicate after
> rebooting. I have no idea what the cause could be. Some of the packages I
> had loaded yesterday (apart from Adegenet) were not loaded today. I guess
> I'll have to be even more paranoid and check that each step of my analysis
> does what is supposed to be doing.
> 
> Cheers,
> 
> Max
> 
> ________________________________
> From: Roman Lu?trik <roman.lustrik at biolitika.si>
> Sent: Tuesday, January 3, 2017 5:44 PM
> To: Tagliamonte,Massimiliano S
> Cc: adegenet-forum at lists.r-forge.r-project.org
> Subject: Re: [adegenet-forum] df2genind function unexpected behavior
> 
> Can you provide a reproducible example?
> 
> FWIW, you can use accessor functions like `tab(genind_obj)` or access the
> other slot through `other(genind_obj)`, e.g.
> 
> library(adegenet)
> 
> data(nancycats)
> 
> other(nancycats)$xy
> 
> or assigning things
> 
> other(nancycats)$xy <- xy_object
> 
> To access genotypes, you can use
> 
> tab(nancycats)
> 
> Cheers,
> Roman
> 
> ________________________________
> From: "Tagliamonte,Massimiliano S" <mstagliamonte at ufl.edu>
> To: "adegenet-forum at lists.r-forge.r-project.org"
> <adegenet-forum at r-forge.wu-wien.ac.at> Sent: Tuesday, January 3, 2017
> 10:36:20 PM
> Subject: Re: [adegenet-forum] df2genind function unexpected behavior
> 
> Update:
> 
> OK, I have replaced the dots (".") in the names with "_", now the order of
> the isolates is maintained. I'll have to keep in mind this behavior. I
> guess it's a bad idea to introduce special characters in my data in R.
-- 
Vojt?ch Zeisek
https://trapa.cz/en/

Department of Botany
Faculty of Science, Charles University
Ben?tsk? 433/2, Prague, 12801, CZ
https://www.natur.cuni.cz/biology/botany/

Institute of Botany, Academy of Sciences
Z?mek 1, Pr?honice, 25243, CZ
http://www.ibot.cas.cz/en/

Czech Republic
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From roman.lustrik at biolitika.si  Wed Jan  4 17:02:28 2017
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Wed, 4 Jan 2017 17:02:28 +0100 (CET)
Subject: [adegenet-forum] df2genind function unexpected behavior
In-Reply-To: <1922273.q79CFg48Aa@tilia>
References: <1483477381184.77044@ufl.edu>
 <672841075.230621.1483483481140.JavaMail.zimbra@biolitika.si>
 <1483542303096.59786@ufl.edu> <1922273.q79CFg48Aa@tilia>
Message-ID: <2038785160.239370.1483545748332.JavaMail.zimbra@biolitika.si>

In my experience, this is very common. Which is important to have a self contained example. I do this for my analyses all the time.

Cheers,
Roman

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

----- Original Message -----
From: "Vojt?ch Zeisek" <vojta at trapa.cz>
To: adegenet-forum at lists.r-forge.r-project.org
Sent: Wednesday, January 4, 2017 4:17:19 PM
Subject: Re: [adegenet-forum] df2genind function unexpected behavior

Hello,
if You load new library and it by coincidence contain a function with same 
name as one of the already loaded functions, the old one is replaced by the 
new one. When loading such library, the R says which functions are replaced. 
This can be common source of problems. Check it.
Sincerely,
V.

Dne st?eda 4. ledna 2017 15:05:03 CET, Tagliamonte,Massimiliano S napsal(a):
> Thank you for your help, Roman,
> 
> By asking me to provide an example you made me realize something. I tried
> again this morning, with exactly the same commands, and could not reproduce
>  the issue. This is weird. It is not the first time it happens though, i.e.
> getting unexpected behavior in R which I could not replicate after
> rebooting. I have no idea what the cause could be. Some of the packages I
> had loaded yesterday (apart from Adegenet) were not loaded today. I guess
> I'll have to be even more paranoid and check that each step of my analysis
> does what is supposed to be doing.
> 
> Cheers,
> 
> Max
> 
> ________________________________
> From: Roman Lu?trik <roman.lustrik at biolitika.si>
> Sent: Tuesday, January 3, 2017 5:44 PM
> To: Tagliamonte,Massimiliano S
> Cc: adegenet-forum at lists.r-forge.r-project.org
> Subject: Re: [adegenet-forum] df2genind function unexpected behavior
> 
> Can you provide a reproducible example?
> 
> FWIW, you can use accessor functions like `tab(genind_obj)` or access the
> other slot through `other(genind_obj)`, e.g.
> 
> library(adegenet)
> 
> data(nancycats)
> 
> other(nancycats)$xy
> 
> or assigning things
> 
> other(nancycats)$xy <- xy_object
> 
> To access genotypes, you can use
> 
> tab(nancycats)
> 
> Cheers,
> Roman
> 
> ________________________________
> From: "Tagliamonte,Massimiliano S" <mstagliamonte at ufl.edu>
> To: "adegenet-forum at lists.r-forge.r-project.org"
> <adegenet-forum at r-forge.wu-wien.ac.at> Sent: Tuesday, January 3, 2017
> 10:36:20 PM
> Subject: Re: [adegenet-forum] df2genind function unexpected behavior
> 
> Update:
> 
> OK, I have replaced the dots (".") in the names with "_", now the order of
> the isolates is maintained. I'll have to keep in mind this behavior. I
> guess it's a bad idea to introduce special characters in my data in R.
-- 
Vojt?ch Zeisek
https://trapa.cz/en/

Department of Botany
Faculty of Science, Charles University
Ben?tsk? 433/2, Prague, 12801, CZ
https://www.natur.cuni.cz/biology/botany/

Institute of Botany, Academy of Sciences
Z?mek 1, Pr?honice, 25243, CZ
http://www.ibot.cas.cz/en/

Czech Republic

_______________________________________________
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

From mstagliamonte at ufl.edu  Wed Jan  4 18:30:19 2017
From: mstagliamonte at ufl.edu (Tagliamonte,Massimiliano S)
Date: Wed, 4 Jan 2017 17:30:19 +0000
Subject: [adegenet-forum] Fw: df2genind function unexpected behavior
In-Reply-To: <2038785160.239370.1483545748332.JavaMail.zimbra@biolitika.si>
References: <1483477381184.77044@ufl.edu>
 <672841075.230621.1483483481140.JavaMail.zimbra@biolitika.si>
 <1483542303096.59786@ufl.edu> <1922273.q79CFg48Aa@tilia>,
 <2038785160.239370.1483545748332.JavaMail.zimbra@biolitika.si>
Message-ID: <1483551019191.21283@ufl.edu>

Thanks for the feedback to the both of you,

Nice to know it's not just me ;) 

Cheers,
Max

________________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at <adegenet-forum-bounces at r-forge.wu-wien.ac.at> on behalf of Roman Lu?trik <roman.lustrik at biolitika.si>
Sent: Wednesday, January 4, 2017 11:02 AM
To: Vojt?ch Zeisek
Cc: adegenet-forum at r-forge.wu-wien.ac.at
Subject: Re: [adegenet-forum] df2genind function unexpected behavior

In my experience, this is very common. Which is important to have a self contained example. I do this for my analyses all the time.

Cheers,
Roman

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

----- Original Message -----
From: "Vojt?ch Zeisek" <vojta at trapa.cz>
To: adegenet-forum at lists.r-forge.r-project.org
Sent: Wednesday, January 4, 2017 4:17:19 PM
Subject: Re: [adegenet-forum] df2genind function unexpected behavior

Hello,
if You load new library and it by coincidence contain a function with same
name as one of the already loaded functions, the old one is replaced by the
new one. When loading such library, the R says which functions are replaced.
This can be common source of problems. Check it.
Sincerely,
V.

Dne st?eda 4. ledna 2017 15:05:03 CET, Tagliamonte,Massimiliano S napsal(a):
> Thank you for your help, Roman,
>
> By asking me to provide an example you made me realize something. I tried
> again this morning, with exactly the same commands, and could not reproduce
>  the issue. This is weird. It is not the first time it happens though, i.e.
> getting unexpected behavior in R which I could not replicate after
> rebooting. I have no idea what the cause could be. Some of the packages I
> had loaded yesterday (apart from Adegenet) were not loaded today. I guess
> I'll have to be even more paranoid and check that each step of my analysis
> does what is supposed to be doing.
>
> Cheers,
>
> Max
>
> ________________________________
> From: Roman Lu?trik <roman.lustrik at biolitika.si>
> Sent: Tuesday, January 3, 2017 5:44 PM
> To: Tagliamonte,Massimiliano S
> Cc: adegenet-forum at lists.r-forge.r-project.org
> Subject: Re: [adegenet-forum] df2genind function unexpected behavior
>
> Can you provide a reproducible example?
>
> FWIW, you can use accessor functions like `tab(genind_obj)` or access the
> other slot through `other(genind_obj)`, e.g.
>
> library(adegenet)
>
> data(nancycats)
>
> other(nancycats)$xy
>
> or assigning things
>
> other(nancycats)$xy <- xy_object
>
> To access genotypes, you can use
>
> tab(nancycats)
>
> Cheers,
> Roman
>
> ________________________________
> From: "Tagliamonte,Massimiliano S" <mstagliamonte at ufl.edu>
> To: "adegenet-forum at lists.r-forge.r-project.org"
> <adegenet-forum at r-forge.wu-wien.ac.at> Sent: Tuesday, January 3, 2017
> 10:36:20 PM
> Subject: Re: [adegenet-forum] df2genind function unexpected behavior
>
> Update:
>
> OK, I have replaced the dots (".") in the names with "_", now the order of
> the isolates is maintained. I'll have to keep in mind this behavior. I
> guess it's a bad idea to introduce special characters in my data in R.
--
Vojt?ch Zeisek
https://trapa.cz/en/

Department of Botany
Faculty of Science, Charles University
Ben?tsk? 433/2, Prague, 12801, CZ
https://www.natur.cuni.cz/biology/botany/

Institute of Botany, Academy of Sciences
Z?mek 1, Pr?honice, 25243, CZ
http://www.ibot.cas.cz/en/

Czech Republic

_______________________________________________
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
_______________________________________________
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

From stakkelsdreng at gmail.com  Tue Jan  3 15:39:39 2017
From: stakkelsdreng at gmail.com (=?UTF-8?Q?Steffen_J=c3=b8rgensen?=)
Date: Tue, 3 Jan 2017 15:39:39 +0100
Subject: [adegenet-forum] DAPC microbiome data
Message-ID: <fb74b760-f2d7-0cf1-fd63-b5007901baf7@gmail.com>

Hi

So ive tried to search through the old posts in the forum to find 
answers to my problem. I am quite new in R, and I am not sure how to 
approach this.

Im working on 16s sequence data. Im looking into the possibles changes 
in the gut microbiome with 3 different treatments. So id like to do a 
DAPC on my data, which ive seen in several  papers, in order to see if 
there are any positive, negative correlation between any of the OTUs and 
how much impact these might have on the composition of the microbiome.

Ive extracted my OTU read frequencies, here in percent, in this small 
test sheet.

My problem is, the previous DAPC ive made have been on binary 1/0 data, 
while in this case, the data is numeric.

I have my data with sample names and OTUs, and i define the groups 
myself and feed the dapc with this. However, im not sure if im doing 
this the right way at all.


Id really apprichiateif anyone have any thoughts, tutorials, scripts or 
link to other forums, which could help me.


Many thanks Steffen


### ive added my code here, with some few notes in

 > data <- .....data.csv

 > data1<-as.data.frame(data)

 > row.names(data1)<-data$OTU

 > data2<-data1[,-1]

 > data2
            control1     control2     control3     control4 control5     
treat1.1     treat1.2     treat1.3     treat1.4 treat1.5
OTU1    0.970819772  0.539721819  3.417332782  0.830027744 1.205602589  
0.023624150  0.024030374  0.052820063  0.125134387 0.063626931
OTU2    0.000000000  0.001066644  0.006534097  0.001146447 0.002826735  
0.000000000  0.000000000  0.000000000  0.000881228 0.000000000
OTU3   12.873793430  8.137426402  3.530590465  4.747437691 12.686387860  
0.048275437  0.036846574  0.017958821  0.014099649 0.021535269
OTU4    0.037553200  0.015999659  0.023958356  0.040125651 0.038160926  
0.031841246  0.096121498  0.021128025  0.017624562 0.037197283
OTU5   11.617847510  4.246309412 42.157994470 12.318574740 13.695532340  
0.632716366  0.885919803  0.849346616  2.390771780 1.175629907
OTU6    0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU7    0.002781719  0.000000000  0.002178032  0.001146447 0.001413368  
0.000000000  0.000000000  0.000000000  0.000000000 0.001957752
OTU8    0.326851929  0.219728646  0.076231133  0.259097058 1.102426752  
0.003081411  0.001602025  0.002112803  0.005287368 0.004894379
OTU9    0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000881228 0.000000000
OTU10   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU11   2.218420540  0.217595358  0.008712129  3.276545984 0.643082272  
0.004108548  1.799074030  0.005282006  0.000000000 0.069500186
OTU12   0.000000000  0.001066644  0.008712129  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.003524912 0.000000000
OTU13   0.000000000  0.001066644  0.000000000  0.002292894 0.000000000  
0.001027137  0.000000000  0.000000000  0.002643684 0.000000000
OTU14   0.006954296  0.002133288  0.000000000  0.002292894 0.004240103  
0.001027137  0.001602025  0.000000000  0.001762456 0.000978876
OTU15   0.000000000  0.001066644  0.000000000  0.003439341 0.002826735  
0.000000000  0.000000000  0.000000000  0.000881228 0.000000000
OTU16   0.001390859  0.002133288  0.000000000  0.000000000 0.001413368  
0.000000000  0.000000000  0.000000000  0.026436842 0.000000000
OTU17   0.000000000  0.001066644  0.000000000  0.000000000 0.001413368  
0.002054274  0.000000000  0.002112803  0.007931053 0.015662014
OTU18   1.799771899  0.070398498  0.023958356  0.003439341 0.008480206  
0.009244233  0.003204050  0.004225605  0.003524912 0.009788759
OTU19   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.018505790 0.001957752
OTU20   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.001056401  0.000000000 0.000978876
OTU21   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU22   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU23   0.009736015  0.004266576  0.010890162  0.010318024 0.019787147  
0.006162822  0.001602025  0.003169204  0.022030702 0.004894379
OTU24   0.000000000  0.000000000  0.000000000  0.000000000 0.001413368  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU25   0.019472030  0.009599795  0.000000000  0.021782496 0.019787147  
0.009244233  0.004806075  0.001056401  0.006168597 0.017619765
OTU26   0.019472030  0.002133288  0.004356065  0.002292894 0.007066838  
0.006162822  0.003204050  0.002112803  0.002643684 0.011746510
OTU27   0.015299452  0.006399863  0.000000000  0.021782496 0.005653471  
0.003081411  0.008010125  0.000000000  0.004406140 0.006852131
OTU28   0.005563437  0.001066644  0.000000000  0.005732236 0.000000000  
0.001027137  0.000000000  0.000000000  0.000000000 0.000978876
OTU29   0.000000000  0.001066644  0.002178032  0.003439341 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU30   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU31   0.000000000  0.000000000  0.000000000  0.000000000 0.004240103  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU32   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU33   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000978876
OTU34   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU35   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU36   0.000000000  0.000000000  0.002178032  0.000000000 0.002826735  
0.002054274  0.000000000  0.000000000  0.000000000 0.000000000
OTU37   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU38   0.000000000  0.000000000  0.002178032  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000881228 0.000978876
OTU39   0.004172578  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU40   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU41   0.001390859  0.005333220  0.000000000  0.001146447 0.014133676  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU42   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU43   0.000000000  0.001066644  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000881228 0.000000000
OTU44   0.026426326  0.018132946  0.008712129  0.063054594 0.107415940  
0.005135685  0.003204050  0.001056401  0.007049825 0.021535269
OTU45   0.001390859  0.000000000  0.000000000  0.000000000 0.004240103  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU46   0.005563437  0.000000000  0.006534097  0.000000000 0.009893573  
0.005135685  0.001602025  0.006338408  0.005287368 0.013704262
OTU47   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU48   0.011126874  0.011733083  0.008712129  0.022928943 0.018373779  
0.004108548  0.003204050  0.003169204  0.002643684 0.008809883
OTU49   0.015299452  0.006399863  0.002178032  0.006878683 0.007066838  
0.002054274  0.000000000  0.001056401  0.003524912 0.008809883
OTU50   0.002781719  0.003199932  0.002178032  0.000000000 0.001413368  
0.000000000  0.000000000  0.000000000  0.000881228 0.000000000
            treat2.1     treat2.2     treat2.3     treat2.4 treat2.5     
treat3.1     treat3.2     treat3.3     treat3.4 treat3.5
OTU1    0.071290944  0.025272583  0.028065955  0.177536027 0.028360174  
0.073765453  0.059841719  0.052010194  0.073526837 0.082378786
OTU2    0.005780347  0.000000000  0.002004711  0.000000000 0.000000000  
0.016392323  0.043385246  0.010402039  0.029760863 0.007845599
OTU3    1.013487476  0.624593833  0.503182479  0.370181502 0.217765623  
2.685608906 12.695420610  7.049114960  5.423479570 1.766567289
OTU4    0.023121387  0.060172816  0.108254398  3.562052619 0.040514535  
0.310088109  0.124171566  0.024271424  0.642484507 1.442282546
OTU5    1.192678227  0.645052591  0.766801985 10.990235520 0.463891421  
1.784031145  2.523824484  1.035002861  3.184412310 3.427218997
OTU6    0.000000000  0.000000000  0.001002356  0.039662304 0.000000000  
0.009562188  0.000000000  0.000000000  0.000000000 0.000000000
OTU7    0.000000000  0.002406913  0.017040044  0.109543506 0.001012863  
0.010928215  0.005984172  0.000000000  0.183817093 0.011768398
OTU8    0.017341040  0.004813825  0.049115421  0.084990651 0.005064317  
0.017758350  0.038897117  0.069346925  0.154056231 0.075840787
OTU9    0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
1.055938802  0.000000000  0.001733673  0.000000000 0.000000000
OTU10   0.000000000  0.000000000  0.000000000  0.000000000 0.003038590  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU11   0.021194605  0.150432041  1.186788954  4.381740231 5.629494581  
0.040980807  0.031416902  0.504498882  0.073526837 0.179141168
OTU12   0.000000000  0.000000000  0.006014133  0.003777362 0.000000000  
0.010928215  0.002992086  0.000000000  0.001750639 0.023536796
OTU13   0.000000000  0.000000000  0.001002356  0.000000000 0.000000000  
0.025954511  0.002992086  0.008668366  0.000000000 0.000000000
OTU14   0.003853565  0.045731340  0.025058888  0.092545376 0.011141497  
0.008196161  0.000000000  0.003467346  0.017506390 0.111145980
OTU15   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.024588484  0.001496043  0.000000000  0.001750639 0.000000000
OTU16   0.000000000  0.000000000  0.000000000  0.018886811 0.000000000  
0.016392323  0.011968344  0.001733673  0.008753195 0.000000000
OTU17   0.001926782  0.001203456  0.000000000  0.000000000 0.000000000  
0.006830135  0.001496043  0.000000000  0.003501278 0.000000000
OTU18   0.001926782  0.007220738  0.085200221  0.000000000 0.006077180  
0.570999249  0.372514699  1.991990430  0.390392493 0.847324651
OTU19   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.004098081  0.000000000  0.001733673  0.001750639 0.000000000
OTU20   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.001366027  0.002992086  0.000000000  0.000000000 0.000000000
OTU21   0.000000000  0.001203456  0.000000000  0.069881202 0.000000000  
0.002732054  0.000000000  0.000000000  0.008753195 0.000000000
OTU22   0.000000000  0.000000000  0.000000000  0.001888681 0.001012863  
0.000000000  0.001496043  0.000000000  0.000000000 0.000000000
OTU23   0.125240848  0.028882952  0.040094221  0.649706310 0.013167224  
0.215832252  0.127163652  0.039874482  0.236336263 0.171295570
OTU24   0.000000000  0.003610369  0.006014133  0.016998130 0.001012863  
0.013660269  0.020944602  0.000000000  0.028010224 0.096762383
OTU25   0.040462428  0.423616627  0.292687816  0.759249816 0.031398764  
0.143432826  0.010472301  0.013869385  0.180315815 1.159840996
OTU26   0.001926782  0.002406913  0.000000000  0.001888681 0.014180087  
0.057373130  0.016456473  0.022537751  0.012254473 0.045765992
OTU27   0.036608863  0.197366838  0.153360397  0.421175893 0.015192950  
0.058739157  0.001496043  0.003467346  0.084030671 0.478581516
OTU28   0.000000000  0.002406913  0.000000000  0.003777362 0.003038590  
0.023222457  0.005984172  0.000000000  0.014005112 0.009153198
OTU29   0.000000000  0.000000000  0.000000000  0.000000000 0.002025727  
0.006830135  0.046377332  0.001733673  0.000000000 0.000000000
OTU30   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.002992086  0.000000000  0.000000000 0.000000000
OTU31   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU32   0.000000000  0.000000000  0.000000000  0.015109449 0.000000000  
0.000000000  0.001496043  0.000000000  0.000000000 0.000000000
OTU33   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.084993985
OTU34   0.000000000  0.001203456  0.006014133  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.008753195 0.000000000
OTU35   0.000000000  0.000000000  0.000000000  0.009443406 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU36   0.000000000  0.000000000  0.016037689  0.000000000 0.001012863  
0.020490404  0.002992086  0.000000000  0.003501278 0.000000000
OTU37   0.000000000  0.000000000  0.000000000  0.001888681 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU38   0.001926782  0.002406913  0.000000000  0.226641736 0.001012863  
0.001366027  0.000000000  0.001733673  0.015755751 0.062764789
OTU39   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.001733673  0.000000000 0.000000000
OTU40   0.000000000  0.000000000  0.000000000  0.000000000 0.002025727  
0.000000000  0.000000000  0.000000000  0.014005112 0.000000000
OTU41   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU42   0.000000000  0.001203456  0.000000000  0.137873723 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.000000000
OTU43   0.000000000  0.000000000  0.001002356  0.353183372 0.000000000  
0.013660269  0.019448559  0.001733673  0.001750639 0.018306397
OTU44   0.055876686  0.363443811  0.363855059  0.846129148 0.018231541  
0.105184072  0.001496043  0.013869385  0.176814537 0.929703436
OTU45   0.000000000  0.000000000  0.001002356  0.092545376 0.005064317  
0.015026296  0.004488129  0.001733673  0.008753195 0.015691197
OTU46   0.001926782  0.000000000  0.002004711  0.003777362 0.000000000  
0.079229561  0.026928773  0.000000000  0.035012780 0.011768398
OTU47   0.003853565  0.000000000  0.000000000  0.013220768 0.000000000  
0.000000000  0.000000000  0.000000000  0.000000000 0.002615200
OTU48   0.003853565  0.016848389  0.003007067  0.000000000 0.001012863  
0.140700772  0.083778406  0.015603058  0.108539617 0.023536796
OTU49   0.003853565  0.021662214  0.003007067  0.000000000 0.001012863  
0.045078888  0.008976258  0.003467346  0.028010224 0.011768398
OTU50   0.000000000  0.000000000  0.000000000  0.000000000 0.000000000  
0.021856431  0.019448559  0.005201019  0.022758307 0.099377583
  [ reached getOption("max.print") -- omitted 213 rows ]


 > groups<- c(rep("control", 5), rep("treat1", 5), rep("treat2", 5), 
rep("treat3", 5))            ##so here i define my own groups which id 
like the DAPC to be base the analysis on - im sure if i can do this?

 > data.frame(names(data2), groups)
    names.data2.  groups
1      control1 control
2      control2 control
3      control3 control
4      control4 control
5      control5 control
6      treat1.1  treat1
7      treat1.2  treat1
8      treat1.3  treat1
9      treat1.4  treat1
10     treat1.5  treat1
11     treat2.1  treat2
12     treat2.2  treat2
13     treat2.3  treat2
14     treat2.4  treat2
15     treat2.5  treat2
16     treat3.1  treat3
17     treat3.2  treat3
18     treat3.3  treat3
19     treat3.4  treat3
20     treat3.5  treat3
 > otu <- as.data.frame(t(data2))

 > treattype <- factor(groups)


 > dapc1 <- dapc(otu, treattype)                                         
     ## so im not sure if its dapc() or dapc.matrix(), furthermore i not 
sure if i fed the command right?!



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From lschiebelhut at ucmerced.edu  Thu Jan  5 08:10:06 2017
From: lschiebelhut at ucmerced.edu (Lauren Schiebelhut)
Date: Wed, 4 Jan 2017 23:10:06 -0800
Subject: [adegenet-forum] Replace NA in genlight file for xvalDapc
Message-ID: <CAAbe=AeyLptUCo=VH7oq=Zo2dU1p3B+hw35R1FwNiEKz4-fGrA@mail.gmail.com>

Hello,

I am trying to replace "NA" in my genlight file to run xvalDapc.

Is there an equivalent of the following command for genlight?
X <- tab(obj, NA.method="mean")

I get the following error when I try it with my file:
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ?tab? for signature
?"genlight"?

I originally tried to use na.replace as is written in section 4.3 of the
DAPC tutorial (dated 2 Sep 2016), but discovered it is not included in
adegenet 2.0.2.

Thank you for your time.

Lauren
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From hiren.ghosh at gmail.com  Tue Jan 10 12:04:25 2017
From: hiren.ghosh at gmail.com (Hiren Ghosh)
Date: Tue, 10 Jan 2017 12:04:25 +0100
Subject: [adegenet-forum] Query about Adegene : How to get snp position
	plateau curve
Message-ID: <CAK5g6T1_62aw3ThSJ39N+dEwTTzBQ6GjvvVTg362TFrGiD5RvA@mail.gmail.com>

Hello Developer, Currently i am using your adegent package,  in this way :
#data input from multi-genome-alignment file
dna <- fasta2DNAbin("./core_gene_alignment.fasta")
D <- dist.dna(dna, model="N")
clust <- gengraph(D)


I would like to have a look how many snps position is there until my data
will be a plateau curve.  . Could you please help me out.


Thanks Advance.




-- 






*Hiren Ghosh, Doctoral Research Scholar Biomedizinisches Forschungszentrum
SeltersbergInstitut f?r Medizinische
MikrobiologieJustus-Liebig-Universit?tSchubertstr. 8135392 Gie?en , Germany*

*Mobile No: 017672157634*

*Email:hiren.ghosh at med.uni-giessen.de*
<Email%3Ahiren.ghosh at med.uni-giessen.de>



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From roman.lustrik at biolitika.si  Tue Jan 10 13:25:12 2017
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Tue, 10 Jan 2017 13:25:12 +0100 (CET)
Subject: [adegenet-forum] Query about Adegene : How to get snp
	position	plateau curve
In-Reply-To: <CAK5g6T1_62aw3ThSJ39N+dEwTTzBQ6GjvvVTg362TFrGiD5RvA@mail.gmail.com>
References: <CAK5g6T1_62aw3ThSJ39N+dEwTTzBQ6GjvvVTg362TFrGiD5RvA@mail.gmail.com>
Message-ID: <1065772872.258804.1484051112302.JavaMail.zimbra@biolitika.si>

What statistic are you trying to square off against number of SNPs? 

Cheers, 
Roman 

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


From: "Hiren Ghosh" <hiren.ghosh at gmail.com> 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Tuesday, January 10, 2017 12:04:25 PM 
Subject: [adegenet-forum] Query about Adegene : How to get snp position plateau curve 

Hello Developer, Currently i am using your adegent package, in this way : 
#data input from multi-genome-alignment file 
dna <- fasta2DNAbin(". /core_gene_alignment. fasta") 
D <- dist.dna(dna, model="N") 
clust <- gengraph(D) 


I would like to have a look how many snps position is there until my data will be a plateau curve. . Could you please help me out. 


Thanks Advance. 




-- 


Hiren Ghosh, Doctoral Research Scholar 
Biomedizinisches Forschungszentrum Seltersberg 
Institut f?r Medizinische Mikrobiologie 
Justus-Liebig-Universit?t 
Schubertstr. 81 
35392 Gie?en , Germany 

Mobile No: 017672157634 

Email:hiren.ghosh at med.uni-giessen.de 



Sent with Mailtrack 

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From roman.lustrik at biolitika.si  Tue Jan 10 13:43:20 2017
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Tue, 10 Jan 2017 13:43:20 +0100 (CET)
Subject: [adegenet-forum] Fwd: Query about Adegene : How to get snp position
 plateau curve
In-Reply-To: <CAK5g6T1LbO5juzx5NU1HaEmxetXVKGO4ygTaVYR3fmsMbqfgxw@mail.gmail.com>
References: <CAK5g6T1_62aw3ThSJ39N+dEwTTzBQ6GjvvVTg362TFrGiD5RvA@mail.gmail.com>
 <1065772872.258804.1484051112302.JavaMail.zimbra@biolitika.si>
 <CAK5g6T1LbO5juzx5NU1HaEmxetXVKGO4ygTaVYR3fmsMbqfgxw@mail.gmail.com>
Message-ID: <1090098172.259014.1484052200472.JavaMail.zimbra@biolitika.si>

Forwarding this to the list. 

It's not clear to me what you would like to measure. Would like to see, given a constant cutoff, when clusters don't change much as you add SNPs? 

Cheers, 
Roman 



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


From: "Hiren Ghosh" <hiren.ghosh at gmail.com> 
To: "Roman Lu?trik" <roman.lustrik at biolitika.si> 
Sent: Tuesday, January 10, 2017 1:33:52 PM 
Subject: Re: [adegenet-forum] Query about Adegene : How to get snp position plateau curve 

Hello, 
I am very new to such analysis. Mainly my aim is to cluster based on the number of mutations separating sequences, classifying them in the same cluster if their distance is less than a given threshold. 
Thanks For reply. 
Kind 
Hiren 



Sent with Mailtrack 

On 10 January 2017 at 13:25, Roman Lu?trik < roman.lustrik at biolitika.si > wrote: 



What statistic are you trying to square off against number of SNPs? 

Cheers, 
Roman 

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


From: "Hiren Ghosh" < hiren.ghosh at gmail.com > 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Tuesday, January 10, 2017 12:04:25 PM 
Subject: [adegenet-forum] Query about Adegene : How to get snp position plateau curve 

Hello Developer, Currently i am using your adegent package, in this way : 
#data input from multi-genome-alignment file 
dna <- fasta2DNAbin(". /core_gene_alignment. fasta") 
D <- dist.dna(dna, model="N") 
clust <- gengraph(D) 


I would like to have a look how many snps position is there until my data will be a plateau curve. . Could you please help me out. 


Thanks Advance. 




-- 


Hiren Ghosh, Doctoral Research Scholar 
Biomedizinisches Forschungszentrum Seltersberg 
Institut f?r Medizinische Mikrobiologie 
Justus-Liebig-Universit?t 
Schubertstr. 81 
35392 Gie?en , Germany 

Mobile No: 017672157634 

Email:hiren.ghosh at med.uni-giessen.de 



Sent with Mailtrack 

_______________________________________________ 
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 






-- 


Hiren Ghosh, Doctoral Research Scholar 
Biomedizinisches Forschungszentrum Seltersberg 
Institut f?r Medizinische Mikrobiologie 
Justus-Liebig-Universit?t 
Schubertstr. 81 
35392 Gie?en , Germany 

Mobile No: 017672157634 

Email:hiren.ghosh at med.uni-giessen.de 

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From hiren.ghosh at gmail.com  Tue Jan 10 14:39:59 2017
From: hiren.ghosh at gmail.com (Hiren Ghosh)
Date: Tue, 10 Jan 2017 14:39:59 +0100
Subject: [adegenet-forum] Query about Adegene : How to get snp position
 plateau curve
In-Reply-To: <1090098172.259014.1484052200472.JavaMail.zimbra@biolitika.si>
References: <CAK5g6T1_62aw3ThSJ39N+dEwTTzBQ6GjvvVTg362TFrGiD5RvA@mail.gmail.com>
 <1065772872.258804.1484051112302.JavaMail.zimbra@biolitika.si>
 <CAK5g6T1LbO5juzx5NU1HaEmxetXVKGO4ygTaVYR3fmsMbqfgxw@mail.gmail.com>
 <1090098172.259014.1484052200472.JavaMail.zimbra@biolitika.si>
Message-ID: <CAK5g6T3LpfYBt=wkqEbbXV7nNw-qarFCbuv2HJ4HXkK0rW9jwQ@mail.gmail.com>

My data set like this : I have a core genome alignment of 240 e coli
genome, which are varying number of snps from ~0-44200. Now i would like to
clustered  all them according to number of snps. Suppose all the genome
share bellow 100 snps will be one cluster so on all bellow 500 will be one
cluster so on.....
Can anyone suggest some idea. how to proceed.
Thanks




 Sent with Mailtrack
<https://mailtrack.io/install?source=signature&lang=en&referral=hiren.ghosh at gmail.com&idSignature=22>

On 10 January 2017 at 13:43, Roman Lu?trik <roman.lustrik at biolitika.si>
wrote:

> Forwarding this to the list.
>
> It's not clear to me what you would like to measure. Would like to see,
> given a constant cutoff, when clusters don't change much as you add SNPs?
>
> Cheers,
> Roman
>
>
>
> ----
> In god we trust, all others bring data.
>
> ------------------------------
> *From: *"Hiren Ghosh" <hiren.ghosh at gmail.com>
> *To: *"Roman Lu?trik" <roman.lustrik at biolitika.si>
> *Sent: *Tuesday, January 10, 2017 1:33:52 PM
> *Subject: *Re: [adegenet-forum] Query about Adegene : How to get snp
> position plateau curve
>
> Hello,
> I am very new to such analysis. Mainly my aim is to cluster based on the
> number of mutations separating sequences, classifying them in the same
> cluster if their distance is less than a given threshold.
> Thanks For reply.
> Kind
> Hiren
>
>
>
>  Sent with Mailtrack
> <https://mailtrack.io/install?source=signature&lang=en&referral=hiren.ghosh at gmail.com&idSignature=22>
>
> On 10 January 2017 at 13:25, Roman Lu?trik <roman.lustrik at biolitika.si>
> wrote:
>
>> What statistic are you trying to square off against number of SNPs?
>>
>> Cheers,
>> Roman
>>
>> ----
>> In god we trust, all others bring data.
>>
>> ------------------------------
>> *From: *"Hiren Ghosh" <hiren.ghosh at gmail.com>
>> *To: *adegenet-forum at lists.r-forge.r-project.org
>> *Sent: *Tuesday, January 10, 2017 12:04:25 PM
>> *Subject: *[adegenet-forum] Query about Adegene : How to get snp
>> position        plateau curve
>>
>> Hello Developer, Currently i am using your adegent package,  in this way :
>> #data input from multi-genome-alignment file
>> dna <- fasta2DNAbin("./core_gene_alignment.fasta")
>> D <- dist.dna(dna, model="N")
>> clust <- gengraph(D)
>>
>>
>> I would like to have a look how many snps position is there until my data
>> will be a plateau curve.  . Could you please help me out.
>>
>>
>> Thanks Advance.
>>
>>
>>
>>
>> --
>>
>>
>>
>>
>>
>>
>> *Hiren Ghosh, Doctoral Research Scholar Biomedizinisches
>> Forschungszentrum SeltersbergInstitut f?r Medizinische
>> MikrobiologieJustus-Liebig-Universit?tSchubertstr. 8135392 Gie?en , Germany*
>>
>> *Mobile No: 017672157634*
>>
>> *Email:hiren.ghosh at med.uni-giessen.de*
>> <Email%3Ahiren.ghosh at med.uni-giessen.de>
>>
>>
>>
>>  Sent with Mailtrack
>> <https://mailtrack.io/install?source=signature&lang=en&referral=hiren.ghosh at gmail.com&idSignature=22>
>>
>> _______________________________________________
>> 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
>>
>
>
>
> --
>
>
>
>
>
>
> *Hiren Ghosh, Doctoral Research Scholar Biomedizinisches Forschungszentrum
> SeltersbergInstitut f?r Medizinische
> MikrobiologieJustus-Liebig-Universit?tSchubertstr. 8135392 Gie?en , Germany*
>
> *Mobile No: 017672157634*
>
> *Email:hiren.ghosh at med.uni-giessen.de*
> <Email%3Ahiren.ghosh at med.uni-giessen.de>
>
>


-- 






*Hiren Ghosh, Doctoral Research Scholar Biomedizinisches Forschungszentrum
SeltersbergInstitut f?r Medizinische
MikrobiologieJustus-Liebig-Universit?tSchubertstr. 8135392 Gie?en , Germany*

*Mobile No: 017672157634*

*Email:hiren.ghosh at med.uni-giessen.de*
<Email%3Ahiren.ghosh at med.uni-giessen.de>
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From thibautjombart at gmail.com  Tue Jan 10 14:56:07 2017
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Tue, 10 Jan 2017 13:56:07 +0000
Subject: [adegenet-forum] Query about Adegene : How to get snp position
 plateau curve
In-Reply-To: <CAK5g6T3LpfYBt=wkqEbbXV7nNw-qarFCbuv2HJ4HXkK0rW9jwQ@mail.gmail.com>
References: <CAK5g6T1_62aw3ThSJ39N+dEwTTzBQ6GjvvVTg362TFrGiD5RvA@mail.gmail.com>
 <1065772872.258804.1484051112302.JavaMail.zimbra@biolitika.si>
 <CAK5g6T1LbO5juzx5NU1HaEmxetXVKGO4ygTaVYR3fmsMbqfgxw@mail.gmail.com>
 <1090098172.259014.1484052200472.JavaMail.zimbra@biolitika.si>
 <CAK5g6T3LpfYBt=wkqEbbXV7nNw-qarFCbuv2HJ4HXkK0rW9jwQ@mail.gmail.com>
Message-ID: <CANPRA+qCrG_xOSxwiSyZYL03kgSmXL8Voz9mMRaiQQ5_xhEWDQ@mail.gmail.com>

Hi,

what you describe sounds like a complete linkage clustering. What you wanna
do is:

1) get hamming distances using dist.dna (you got that already)
2) use hclust specifying the right method for complete linkage clustering
3) use cutree on the resulting dendrogram for a given threshold

Cheers
Thibaut


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

On 10 January 2017 at 13:39, Hiren Ghosh <hiren.ghosh at gmail.com> wrote:

> My data set like this : I have a core genome alignment of 240 e coli
> genome, which are varying number of snps from ~0-44200. Now i would like to
> clustered  all them according to number of snps. Suppose all the genome
> share bellow 100 snps will be one cluster so on all bellow 500 will be one
> cluster so on.....
> Can anyone suggest some idea. how to proceed.
> Thanks
>
>
>
>
>  Sent with Mailtrack
> <https://mailtrack.io/install?source=signature&lang=en&referral=hiren.ghosh at gmail.com&idSignature=22>
>
> On 10 January 2017 at 13:43, Roman Lu?trik <roman.lustrik at biolitika.si>
> wrote:
>
>> Forwarding this to the list.
>>
>> It's not clear to me what you would like to measure. Would like to see,
>> given a constant cutoff, when clusters don't change much as you add SNPs?
>>
>> Cheers,
>> Roman
>>
>>
>>
>> ----
>> In god we trust, all others bring data.
>>
>> ------------------------------
>> *From: *"Hiren Ghosh" <hiren.ghosh at gmail.com>
>> *To: *"Roman Lu?trik" <roman.lustrik at biolitika.si>
>> *Sent: *Tuesday, January 10, 2017 1:33:52 PM
>> *Subject: *Re: [adegenet-forum] Query about Adegene : How to get snp
>> position plateau curve
>>
>> Hello,
>> I am very new to such analysis. Mainly my aim is to cluster based on the
>> number of mutations separating sequences, classifying them in the same
>> cluster if their distance is less than a given threshold.
>> Thanks For reply.
>> Kind
>> Hiren
>>
>>
>>
>>  Sent with Mailtrack
>> <https://mailtrack.io/install?source=signature&lang=en&referral=hiren.ghosh at gmail.com&idSignature=22>
>>
>> On 10 January 2017 at 13:25, Roman Lu?trik <roman.lustrik at biolitika.si>
>> wrote:
>>
>>> What statistic are you trying to square off against number of SNPs?
>>>
>>> Cheers,
>>> Roman
>>>
>>> ----
>>> In god we trust, all others bring data.
>>>
>>> ------------------------------
>>> *From: *"Hiren Ghosh" <hiren.ghosh at gmail.com>
>>> *To: *adegenet-forum at lists.r-forge.r-project.org
>>> *Sent: *Tuesday, January 10, 2017 12:04:25 PM
>>> *Subject: *[adegenet-forum] Query about Adegene : How to get snp
>>> position        plateau curve
>>>
>>> Hello Developer, Currently i am using your adegent package,  in this way
>>> :
>>> #data input from multi-genome-alignment file
>>> dna <- fasta2DNAbin("./core_gene_alignment.fasta")
>>> D <- dist.dna(dna, model="N")
>>> clust <- gengraph(D)
>>>
>>>
>>> I would like to have a look how many snps position is there until my
>>> data will be a plateau curve.  . Could you please help me out.
>>>
>>>
>>> Thanks Advance.
>>>
>>>
>>>
>>>
>>> --
>>>
>>>
>>>
>>>
>>>
>>>
>>> *Hiren Ghosh, Doctoral Research Scholar Biomedizinisches
>>> Forschungszentrum SeltersbergInstitut f?r Medizinische
>>> MikrobiologieJustus-Liebig-Universit?tSchubertstr. 8135392 Gie?en , Germany*
>>>
>>> *Mobile No: 017672157634*
>>>
>>> *Email:hiren.ghosh at med.uni-giessen.de*
>>> <Email%3Ahiren.ghosh at med.uni-giessen.de>
>>>
>>>
>>>
>>>  Sent with Mailtrack
>>> <https://mailtrack.io/install?source=signature&lang=en&referral=hiren.ghosh at gmail.com&idSignature=22>
>>>
>>> _______________________________________________
>>> 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
>>>
>>
>>
>>
>> --
>>
>>
>>
>>
>>
>>
>> *Hiren Ghosh, Doctoral Research Scholar Biomedizinisches
>> Forschungszentrum SeltersbergInstitut f?r Medizinische
>> MikrobiologieJustus-Liebig-Universit?tSchubertstr. 8135392 Gie?en , Germany*
>>
>> *Mobile No: 017672157634*
>>
>> *Email:hiren.ghosh at med.uni-giessen.de*
>> <Email%3Ahiren.ghosh at med.uni-giessen.de>
>>
>>
>
>
> --
>
>
>
>
>
>
> *Hiren Ghosh, Doctoral Research Scholar Biomedizinisches Forschungszentrum
> SeltersbergInstitut f?r Medizinische
> MikrobiologieJustus-Liebig-Universit?tSchubertstr. 8135392 Gie?en , Germany*
>
> *Mobile No: 017672157634*
>
> *Email:hiren.ghosh at med.uni-giessen.de*
> <Email%3Ahiren.ghosh at med.uni-giessen.de>
>
> _______________________________________________
> 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 hiren.ghosh at gmail.com  Wed Jan 11 14:21:32 2017
From: hiren.ghosh at gmail.com (Hiren Ghosh)
Date: Wed, 11 Jan 2017 14:21:32 +0100
Subject: [adegenet-forum] Query about Adegene : How to get snp position
 plateau curve
In-Reply-To: <CANPRA+qCrG_xOSxwiSyZYL03kgSmXL8Voz9mMRaiQQ5_xhEWDQ@mail.gmail.com>
References: <CAK5g6T1_62aw3ThSJ39N+dEwTTzBQ6GjvvVTg362TFrGiD5RvA@mail.gmail.com>
 <1065772872.258804.1484051112302.JavaMail.zimbra@biolitika.si>
 <CAK5g6T1LbO5juzx5NU1HaEmxetXVKGO4ygTaVYR3fmsMbqfgxw@mail.gmail.com>
 <1090098172.259014.1484052200472.JavaMail.zimbra@biolitika.si>
 <CAK5g6T3LpfYBt=wkqEbbXV7nNw-qarFCbuv2HJ4HXkK0rW9jwQ@mail.gmail.com>
 <CANPRA+qCrG_xOSxwiSyZYL03kgSmXL8Voz9mMRaiQQ5_xhEWDQ@mail.gmail.com>
Message-ID: <CAK5g6T0wk_RwrCR6qM_Or-_phgEEb3eb4aZUQ0D2mh8soGRR4w@mail.gmail.com>

Hi I was trying to label off from the plot. Can anyone suggest how to
preceded. I tried like


> plot(clust$g, main="Clusters obtained by gengraph", labels=FALSE)
Error in i.parse.plot.params(graph, list(...)) :
  Unknown plot parameters: labels

[image: Inline images 2]



 Sent with Mailtrack

On 10 January 2017 at 14:56, Thibaut Jombart <thibautjombart at gmail.com>
wrote:
>
> Hi,
>
> what you describe sounds like a complete linkage clustering. What you
wanna do is:
>
> 1) get hamming distances using dist.dna (you got that already)
> 2) use hclust specifying the right method for complete linkage clustering
> 3) use cutree on the resulting dendrogram for a given threshold
>
> Cheers
> Thibaut
>
>
> --
> Dr Thibaut Jombart
> Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
> Head of RECON: repidemicsconsortium.org
> sites.google.com/site/thibautjombart/
> github.com/thibautjombart
> Twitter: @TeebzR
> +44(0)20 7594 3658
>
> On 10 January 2017 at 13:39, Hiren Ghosh <hiren.ghosh at gmail.com> wrote:
>>
>> My data set like this : I have a core genome alignment of 240 e coli
genome, which are varying number of snps from ~0-44200. Now i would like to
clustered  all them according to number of snps. Suppose all the genome
share bellow 100 snps will be one cluster so on all bellow 500 will be one
cluster so on.....
>> Can anyone suggest some idea. how to proceed.
>> Thanks
>>
>>
>>
>>
>>  Sent with Mailtrack
>>
>> On 10 January 2017 at 13:43, Roman Lu?trik <roman.lustrik at biolitika.si>
wrote:
>>>
>>> Forwarding this to the list.
>>>
>>> It's not clear to me what you would like to measure. Would like to see,
given a constant cutoff, when clusters don't change much as you add SNPs?
>>>
>>> Cheers,
>>> Roman
>>>
>>>
>>>
>>> ----
>>> In god we trust, all others bring data.
>>>
>>> ________________________________
>>> From: "Hiren Ghosh" <hiren.ghosh at gmail.com>
>>> To: "Roman Lu?trik" <roman.lustrik at biolitika.si>
>>> Sent: Tuesday, January 10, 2017 1:33:52 PM
>>> Subject: Re: [adegenet-forum] Query about Adegene : How to get snp
position plateau curve
>>>
>>> Hello,
>>> I am very new to such analysis. Mainly my aim is to cluster based on
the number of mutations separating sequences, classifying them in the same
cluster if their distance is less than a given threshold.
>>> Thanks For reply.
>>> Kind
>>> Hiren
>>>
>>>
>>>
>>>  Sent with Mailtrack
>>>
>>> On 10 January 2017 at 13:25, Roman Lu?trik <roman.lustrik at biolitika.si>
wrote:
>>>>
>>>> What statistic are you trying to square off against number of SNPs?
>>>>
>>>> Cheers,
>>>> Roman
>>>>
>>>> ----
>>>> In god we trust, all others bring data.
>>>>
>>>> ________________________________
>>>> From: "Hiren Ghosh" <hiren.ghosh at gmail.com>
>>>> To: adegenet-forum at lists.r-forge.r-project.org
>>>> Sent: Tuesday, January 10, 2017 12:04:25 PM
>>>> Subject: [adegenet-forum] Query about Adegene : How to get snp
position        plateau curve
>>>>
>>>> Hello Developer, Currently i am using your adegent package,  in this
way :
>>>> #data input from multi-genome-alignment file
>>>> dna <- fasta2DNAbin("./core_gene_alignment.fasta")
>>>> D <- dist.dna(dna, model="N")
>>>> clust <- gengraph(D)
>>>>
>>>>
>>>> I would like to have a look how many snps position is there until my
data will be a plateau curve.  . Could you please help me out.
>>>>
>>>>
>>>> Thanks Advance.
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> Hiren Ghosh, Doctoral Research Scholar
>>>> Biomedizinisches Forschungszentrum Seltersberg
>>>> Institut f?r Medizinische Mikrobiologie
>>>> Justus-Liebig-Universit?t
>>>> Schubertstr. 81
>>>> 35392 Gie?en , Germany
>>>>
>>>> Mobile No: 017672157634
>>>>
>>>> Email:hiren.ghosh at med.uni-giessen.de
>>>>
>>>>
>>>>
>>>>
>>>>  Sent with Mailtrack
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>>
>>>
>>>
>>> --
>>>
>>> Hiren Ghosh, Doctoral Research Scholar
>>> Biomedizinisches Forschungszentrum Seltersberg
>>> Institut f?r Medizinische Mikrobiologie
>>> Justus-Liebig-Universit?t
>>> Schubertstr. 81
>>> 35392 Gie?en , Germany
>>>
>>> Mobile No: 017672157634
>>>
>>> Email:hiren.ghosh at med.uni-giessen.de
>>>
>>>
>>
>>
>>
>> --
>>
>> Hiren Ghosh, Doctoral Research Scholar
>> Biomedizinisches Forschungszentrum Seltersberg
>> Institut f?r Medizinische Mikrobiologie
>> Justus-Liebig-Universit?t
>> Schubertstr. 81
>> 35392 Gie?en , Germany
>>
>> Mobile No: 017672157634
>>
>> Email:hiren.ghosh at med.uni-giessen.de
>>
>>
>> _______________________________________________
>> 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
>
>



--

Hiren Ghosh, Doctoral Research Scholar
Biomedizinisches Forschungszentrum Seltersberg
Institut f?r Medizinische Mikrobiologie
Justus-Liebig-Universit?t
Schubertstr. 81
35392 Gie?en , Germany

Mobile No: 017672157634

Email:hiren.ghosh at med.uni-giessen.de
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From M.Ruhsam at rbge.ac.uk  Wed Jan 11 10:52:46 2017
From: M.Ruhsam at rbge.ac.uk (Markus Ruhsam)
Date: Wed, 11 Jan 2017 09:52:46 +0000
Subject: [adegenet-forum] Very different numbers in groups with same
 paramters using find.clusters
Message-ID: <6597957BE88F22419CB987B2E084C50504EF740AA04D@MBX-EXC-ED-01.rbge.org.uk>

Hello,

I want to do a DAPC on a dataset containing 1548 SNPs starting with the find.clusters command but get wildly different numbers in each group when I repeat the command using exactly the same parameters. Does anybody have an explanation for this?

Thank you

Markus


> grp <- find.clusters(rul, max.n.clust=10)

Choose the number PCs to retain (>=1):

400

Choose the number of clusters (>=2:

3

> table(pop(rul), grp$grp)



               1   2   3

  native       2 131  52

  non-native  67   3   1

  hispanica    5   0   0

  odd         12 113  41



> grp <- find.clusters(rul, max.n.clust=10)

Choose the number PCs to retain (>=1):

400

Choose the number of clusters (>=2:

3

> table(pop(rul), grp$grp)



               1   2   3

  native       1   1 183

  non-native  15  51   5

  hispanica    0   5   0

  odd          0  12 154



> grp <- find.clusters(rul, max.n.clust=10)

Choose the number PCs to retain (>=1):

400

Choose the number of clusters (>=2:

3

> table(pop(rul), grp$grp)



               1   2   3

  native      49 134   2

  non-native   1   3  67

  hispanica    0   0   5

  odd         41 113  12







Dr Markus Ruhsam
Molecular Plant Ecologist
Royal Botanic Garden Edinburgh
20A Inverleith Row
Edinburgh
EH3 5LR
United Kingdom

Tel: +44 (0) 131 248 2859
Fax: +44 (0) 131 248 2901

http://www.rbge.org.uk/science/genetics-and-conservation/markus-ruhsam-homepage

The mission of the Royal Botanic Garden Edinburgh is to "To explore, conserve and explain the world of plants for a better future"


[cid:image001.png at 01D26BEF.A833AB80]

The Royal Botanic Garden Edinburgh is a charity registered in Scotland (No SC007983)
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From mbzandi at znu.ac.ir  Thu Jan 12 23:25:58 2017
From: mbzandi at znu.ac.ir (mbzandi at znu.ac.ir)
Date: Thu, 12 Jan 2017 22:25:58 +0000
Subject: [adegenet-forum] Question about the import SNP data to adegenet via
	read.PLINK
In-Reply-To: <CAK5g6T0wk_RwrCR6qM_Or-_phgEEb3eb4aZUQ0D2mh8soGRR4w@mail.gmail.com>
References: <CAK5g6T1_62aw3ThSJ39N+dEwTTzBQ6GjvvVTg362TFrGiD5RvA@mail.gmail.com>
 <1065772872.258804.1484051112302.JavaMail.zimbra@biolitika.si>
 <CAK5g6T1LbO5juzx5NU1HaEmxetXVKGO4ygTaVYR3fmsMbqfgxw@mail.gmail.com>
 <1090098172.259014.1484052200472.JavaMail.zimbra@biolitika.si>
 <CAK5g6T3LpfYBt=wkqEbbXV7nNw-qarFCbuv2HJ4HXkK0rW9jwQ@mail.gmail.com>
 <CANPRA+qCrG_xOSxwiSyZYL03kgSmXL8Voz9mMRaiQQ5_xhEWDQ@mail.gmail.com>
 <CAK5g6T0wk_RwrCR6qM_Or-_phgEEb3eb4aZUQ0D2mh8soGRR4w@mail.gmail.com>
Message-ID: <cbc5824f7e2d5b47af66563cba13cf96@mail.znu.ac.ir>

Dear All,
I am trying to apply the Discriminant Analysis of Principal Components (DAPC ) for my SNP dataset.
Here I used the following command line to import data to adegenet R package, but I have a problem and I got the error.
I attached my data files include the PLINK.raw and map file.
>  extract.PLINKmap(?phase.map?, x = NULL)
Error in factor(txt[ord, 1]) : object 'ord' not found
> x
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From thibautjombart at gmail.com  Mon Jan 16 12:34:12 2017
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Mon, 16 Jan 2017 11:34:12 +0000
Subject: [adegenet-forum] Very different numbers in groups with same
 paramters using find.clusters
In-Reply-To: <6597957BE88F22419CB987B2E084C50504EF740AA04D@MBX-EXC-ED-01.rbge.org.uk>
References: <6597957BE88F22419CB987B2E084C50504EF740AA04D@MBX-EXC-ED-01.rbge.org.uk>
Message-ID: <CANPRA+rVx+YFBQFx5iTAVaAwP-a0Kf_eNg48ccEJymwOFXoPPA@mail.gmail.com>

Hello,

the K-means algorithm, used in find.clusters, uses random initial
conditions which may lead to converging to different solutions. This can be
the case if the data is noisy, and typically is the case when there are no
clusters.

The usual way to stabilise the results is increase the number of starting
points, which I think defaults to 10. Try setting n.start = 50 - that may
help.

Best
Thibaut


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

On 11 January 2017 at 09:52, Markus Ruhsam <M.Ruhsam at rbge.ac.uk> wrote:

> Hello,
>
>
>
> I want to do a DAPC on a dataset containing 1548 SNPs starting with the
> find.clusters command but get wildly different numbers in each group when I
> repeat the command using exactly the same parameters. Does anybody have an
> explanation for this?
>
>
>
> Thank you
>
>
>
> Markus
>
>
>
> > grp <- find.clusters(rul, max.n.clust=10)
>
> Choose the number PCs to retain (>=1):
>
> 400
>
> Choose the number of clusters (>=2:
>
> 3
>
> > table(pop(rul), grp$grp)
>
>
>
>                1   2   3
>
>   native       2 131  52
>
>   non-native  67   3   1
>
>   hispanica    5   0   0
>
>   odd         12 113  41
>
>
>
> > grp <- find.clusters(rul, max.n.clust=10)
>
> Choose the number PCs to retain (>=1):
>
> 400
>
> Choose the number of clusters (>=2:
>
> 3
>
> > table(pop(rul), grp$grp)
>
>
>
>                1   2   3
>
>   native       1   1 183
>
>   non-native  15  51   5
>
>   hispanica    0   5   0
>
>   odd          0  12 154
>
>
>
> > grp <- find.clusters(rul, max.n.clust=10)
>
> Choose the number PCs to retain (>=1):
>
> 400
>
> Choose the number of clusters (>=2:
>
> 3
>
> > table(pop(rul), grp$grp)
>
>
>
>                1   2   3
>
>   native      49 134   2
>
>   non-native   1   3  67
>
>   hispanica    0   0   5
>
>   odd         41 113  12
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Dr Markus Ruhsam
>
> Molecular Plant Ecologist
>
> Royal Botanic Garden Edinburgh
>
> 20A Inverleith Row
>
> Edinburgh
>
> EH3 5LR
>
> United Kingdom
>
>
>
> Tel: +44 (0) 131 248 2859 <+44%20131%20248%202859>
> Fax: +44 (0) 131 248 2901 <+44%20131%20248%202901>
>
>
>
> http://www.rbge.org.uk/science/genetics-and-conservation/markus-ruhsam-
> homepage
>
>
>
> The mission of the Royal Botanic Garden Edinburgh is to ?*To explore,
> conserve and explain the world of plants for a better future*?
>
>
>
>
>
> [image: cid:image002.png at 01D09F78.9DFBA130]
>
>
>
>
> The Royal Botanic Garden Edinburgh <http://www.rbge.org.uk/> is a charity
> registered in Scotland (No SC007983)
>
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/
> listinfo/adegenet-forum
>
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From M.Ruhsam at rbge.ac.uk  Mon Jan 16 15:35:24 2017
From: M.Ruhsam at rbge.ac.uk (Markus Ruhsam)
Date: Mon, 16 Jan 2017 14:35:24 +0000
Subject: [adegenet-forum] Different outcomes using dapc(x,
	grp$grp) and dapc(x)
Message-ID: <6597957BE88F22419CB987B2E084C50504EFA651CE16@MBX-EXC-ED-01.rbge.org.uk>

Hello,

I followed the DAPC tutorial and produced a scatter plot using the following commands

> rul<-read.structure("1548SNPsQ60_427_scc30_sec10_nuclear_195ampl.str",missing=-9,quiet=FALSE)

> grp <- find.clusters(rul, max.n.clust=10, n.start=200)
Choose the number PCs to retain (>=1):
400
Choose the number of clusters (>=2:
4
> dapcgrp1 <- dapc(rul, grp$grp)
Choose the number PCs to retain (>=1):
15
Choose the number discriminant functions to retain (>=1):
3
> scatter(dapcgrp1, scree.da=FALSE, solid=1)



[cid:image004.jpg at 01D27005.C5EFCC20]


If I do the same thing without the find.clusters step using the following commands I get quite a different scatter plot


> dapc1 <- dapc(rul)

Choose the number PCs to retain (>=1):

15

Choose the number discriminant functions to retain (>=1):

3

> scatter(dapc1, scree.da=FALSE, solid=1)

[cid:image006.jpg at 01D27005.C5EFCC20]

Although the two plots look somehow similar, the contents and overlap of the groups is different. For example, none of the samples in 'Group 2' (dapc(x, grp$grp)) are in 'hispanica' (dapc(x)) - Group 2 and hispanica are the two small outlier groups occupying the 'same' space in the two DAPC analyses. Looking at the inferred/original table it's obvious that with dapc(x, grp$grp) samples in my predefined 'hispanica' group are put together with other samples into group 3 (where most of my 'non-native' samples fall), whereas with dapc(x) they more or less are in their own group (which makes biological sense).


[cid:image009.jpg at 01D27005.C5EFCC20]
dapc(x, grp$grp)




[cid:image013.jpg at 01D27005.C5EFCC20]
dapc(x)


This raises the question why the two analyses of the same data set produce rather different results and which one should 'believe'? Any help or ideas are appreciated.

Thank you

Markus



Dr Markus Ruhsam
Molecular Plant Ecologist
Royal Botanic Garden Edinburgh
20A Inverleith Row
Edinburgh
EH3 5LR
United Kingdom

Tel: +44 (0) 131 248 2859
Fax: +44 (0) 131 248 2901

http://www.rbge.org.uk/science/genetics-and-conservation/markus-ruhsam-homepage

The mission of the Royal Botanic Garden Edinburgh is to "To explore, conserve and explain the world of plants for a better future"


[cid:image001.png at 01D26FFF.59E41870]

The Royal Botanic Garden Edinburgh is a charity registered in Scotland (No SC007983)
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From thibautjombart at gmail.com  Sat Jan 21 16:24:26 2017
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Sat, 21 Jan 2017 15:24:26 +0000
Subject: [adegenet-forum] Replace NA in genlight file for xvalDapc
In-Reply-To: <CAAbe=AeyLptUCo=VH7oq=Zo2dU1p3B+hw35R1FwNiEKz4-fGrA@mail.gmail.com>
References: <CAAbe=AeyLptUCo=VH7oq=Zo2dU1p3B+hw35R1FwNiEKz4-fGrA@mail.gmail.com>
Message-ID: <CANPRA+p_0wQKqdj1X9k_keXCb-=j=RXc2Bu5-qmZJ6+BTcBJcQ@mail.gmail.com>

Hi Lauren

Sorry I am just catching up with this. Can you file an issue on github?

Cheers
Thibaut


On 10 Jan 2017 12:02 pm, "Lauren Schiebelhut" <lschiebelhut at ucmerced.edu>
wrote:

Hello,

I am trying to replace "NA" in my genlight file to run xvalDapc.

Is there an equivalent of the following command for genlight?
X <- tab(obj, NA.method="mean")

I get the following error when I try it with my file:
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ?tab? for signature
?"genlight"?

I originally tried to use na.replace as is written in section 4.3 of the
DAPC tutorial (dated 2 Sep 2016), but discovered it is not included in
adegenet 2.0.2.

Thank you for your time.

Lauren

_______________________________________________
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 rnsarma at aau.ac.in  Tue Jan 24 06:40:31 2017
From: rnsarma at aau.ac.in (Ramendra Nath Sarma)
Date: Tue, 24 Jan 2017 11:10:31 +0530
Subject: [adegenet-forum] Error in using adegenetServer(what = "DAPC")
Message-ID: <CANpTdqW0Ofi7_f=jr9t=eohP4ikz9urJLn6m0d4FxsRBQKy+rg@mail.gmail.com>

When I am loading my csv file, I have seen an message without any output
that "unable to find an inherited method for function ?tab? for signature
?"NULL"?.

-- 
----------------------------------------------------------------------------------------------------------------------------------------






*Dr R N SarmaProfessorDepartment of Plant Breeding and GeneticsAssam
Agricultural UniversityJorhat-785013Assam, Indiaweb: www.aau.ac.in;
<http://www.aaau.ac.in> Phone: +91-376-2310526; +91-376231133(R);
9435350529(M)*
--------------------------------------------------------------------------------------------------------------------------
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From hiren.ghosh at gmail.com  Fri Jan 27 10:32:18 2017
From: hiren.ghosh at gmail.com (Hiren Ghosh)
Date: Fri, 27 Jan 2017 10:32:18 +0100
Subject: [adegenet-forum] Query about Adegene : How to get snp position
 plateau curve
In-Reply-To: <CANPRA+qCrG_xOSxwiSyZYL03kgSmXL8Voz9mMRaiQQ5_xhEWDQ@mail.gmail.com>
References: <CAK5g6T1_62aw3ThSJ39N+dEwTTzBQ6GjvvVTg362TFrGiD5RvA@mail.gmail.com>
 <1065772872.258804.1484051112302.JavaMail.zimbra@biolitika.si>
 <CAK5g6T1LbO5juzx5NU1HaEmxetXVKGO4ygTaVYR3fmsMbqfgxw@mail.gmail.com>
 <1090098172.259014.1484052200472.JavaMail.zimbra@biolitika.si>
 <CAK5g6T3LpfYBt=wkqEbbXV7nNw-qarFCbuv2HJ4HXkK0rW9jwQ@mail.gmail.com>
 <CANPRA+qCrG_xOSxwiSyZYL03kgSmXL8Voz9mMRaiQQ5_xhEWDQ@mail.gmail.com>
Message-ID: <CAK5g6T3muJhY0Tj=H3he4RfTbHK9yB5xpb5aDQ1Uztc2GhoHKA@mail.gmail.com>

Sorry again, i got some error on hclust package.

here is my try and error
> hclust(distdna, method="complete")
Error in if (is.na(n) || n > 65536L) stop("size cannot be NA nor exceed
65536") : missing value where TRUE/FALSE needed

 > hc <-hclust(dist.dna) Error in if (is.na(n) || n > 65536L) stop("size
cannot be NA nor exceed 65536") : missing value where TRUE/FALSE needed

 > cluster = hclust(dist.dna, method="single") Error in if (is.na(n) || n >
65536L) stop("size cannot be NA nor exceed 65536") : missing value where
TRUE/FALSE needed
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From roman.lustrik at biolitika.si  Fri Jan 27 10:54:11 2017
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Fri, 27 Jan 2017 10:54:11 +0100 (CET)
Subject: [adegenet-forum] Query about Adegene : How to get snp position
 plateau curve
In-Reply-To: <CAK5g6T3muJhY0Tj=H3he4RfTbHK9yB5xpb5aDQ1Uztc2GhoHKA@mail.gmail.com>
References: <CAK5g6T1_62aw3ThSJ39N+dEwTTzBQ6GjvvVTg362TFrGiD5RvA@mail.gmail.com>
 <1065772872.258804.1484051112302.JavaMail.zimbra@biolitika.si>
 <CAK5g6T1LbO5juzx5NU1HaEmxetXVKGO4ygTaVYR3fmsMbqfgxw@mail.gmail.com>
 <1090098172.259014.1484052200472.JavaMail.zimbra@biolitika.si>
 <CAK5g6T3LpfYBt=wkqEbbXV7nNw-qarFCbuv2HJ4HXkK0rW9jwQ@mail.gmail.com>
 <CANPRA+qCrG_xOSxwiSyZYL03kgSmXL8Voz9mMRaiQQ5_xhEWDQ@mail.gmail.com>
 <CAK5g6T3muJhY0Tj=H3he4RfTbHK9yB5xpb5aDQ1Uztc2GhoHKA@mail.gmail.com>
Message-ID: <1691740262.327182.1485510851711.JavaMail.zimbra@biolitika.si>

Please provide a reproducible example (http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example). 

Cheers, 
Roman 

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


From: "Hiren Ghosh" <hiren.ghosh at gmail.com> 
To: "Thibaut Jombart" <thibautjombart at gmail.com>, "Roman Lu?trik" <roman.lustrik at biolitika.si>, adegenet-forum at lists.r-forge.r-project.org 
Sent: Friday, January 27, 2017 10:32:18 AM 
Subject: Re: [adegenet-forum] Query about Adegene : How to get snp position plateau curve 

Sorry again, i got some error on hclust package. 

here is my try and error 
> hclust(distdna, method="complete") 
Error in if ( is.na (n) || n > 65536L) stop("size cannot be NA nor exceed 65536") : missing value where TRUE/FALSE needed 

> hc <-hclust(dist.dna) Error in if ( is.na (n) || n > 65536L) stop("size cannot be NA nor exceed 65536") : missing value where TRUE/FALSE needed 

> cluster = hclust(dist.dna, method="single") Error in if ( is.na (n) || n > 65536L) stop("size cannot be NA nor exceed 65536") : missing value where TRUE/FALSE needed 

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From chadsmith at utexas.edu  Mon Jan 30 16:39:41 2017
From: chadsmith at utexas.edu (Chad Smith)
Date: Mon, 30 Jan 2017 09:39:41 -0600
Subject: [adegenet-forum] polyploids sPCA plot failure
Message-ID: <CAPiVUbhQjOhKcukvh8H8-APXCOaHpgLwLgrkdg6Q04MGEVje1g@mail.gmail.com>

I have a polyploid data set with different ploidy levels for different
individuals.

When plotting the spca object I get "arguments imply differing number of
rows" and a multispati "There are only 21 positive factors" error. The
eigenvalues decomposition plot does not appear.

Please advise on how to troubleshoot this problem. There were no errors
creating the sPCA object. Thanks!

> atm1.spca.2
    ########################################
    # spatial Principal Component Analysis #
    ########################################
class: spca
$call: spca(obj = obj, type = 2)

$nfposi: 3 axis-components saved
$nfnega: 4 axis-components saved
Positive eigenvalues: 0.136 0.0168 0.014 0.0101 0.00731 ...
Negative eigenvalues: -0.00324 -0.0021 -0.0016 -0.00143 -0.000756 ...

  vector length mode    content
1 $eig   39     numeric eigenvalues

  data.frame nrow ncol
content
1 $c1        79   7    principal axes: scaled vectors of alleles
loadings
2 $li        118  7    principal components: coordinates of entities
('scores')
3 $ls        118  7    lag vector of principal
components
4 $as        2    7    pca axes onto spca
axes

$xy: matrix of spatial coordinates
$lw: a list of spatial weights (class 'listw')

other elements: NULL
> plot(atm1.spca.2)
Error in data.frame(eig = eig, var = varspa, moran = moran/varspa) :
  arguments imply differing number of rows: 39, 38
In addition: Warning message:
In multispati(dudi = dudi, listw = lw, scannf = FALSE, nfposi = nfposimax,
:
  There are only 21 positive factors.
>

Cheers,
Chad

-- 
Chad Smith
Postdoctoral Fellow
Dept of Integrative Biology
University of Texas at Austin
1 University Station C0990
Austin, TX 78712

Office: PAT 632
Phone: 512-471-7619
Fax: 512-471-3878
https://chadcsmith.wordpress.com/
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From roman.lustrik at biolitika.si  Tue Jan 31 09:34:37 2017
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Tue, 31 Jan 2017 09:34:37 +0100 (CET)
Subject: [adegenet-forum] polyploids sPCA plot failure
In-Reply-To: <CAPiVUbhQjOhKcukvh8H8-APXCOaHpgLwLgrkdg6Q04MGEVje1g@mail.gmail.com>
References: <CAPiVUbhQjOhKcukvh8H8-APXCOaHpgLwLgrkdg6Q04MGEVje1g@mail.gmail.com>
Message-ID: <616164445.333268.1485851677446.JavaMail.zimbra@biolitika.si>

Can you make this reproducible and post it to github (https://github.com/thibautjombart/adegenet/issues)? 

Cheers, 
Roman 

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


From: "Chad Smith" <chadsmith at utexas.edu> 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Monday, January 30, 2017 4:39:41 PM 
Subject: [adegenet-forum] polyploids sPCA plot failure 

I have a polyploid data set with different ploidy levels for different individuals. 

When plotting the spca object I get "arguments imply differing number of rows" and a multispati "There are only 21 positive factors" error. The eigenvalues decomposition plot does not appear. 

Please advise on how to troubleshoot this problem. There were no errors creating the sPCA object. Thanks! 

> atm1.spca.2 
######################################## 
# spatial Principal Component Analysis # 
######################################## 
class: spca 
$call: spca(obj = obj, type = 2) 

$nfposi: 3 axis-components saved 
$nfnega: 4 axis-components saved 
Positive eigenvalues: 0.136 0.0168 0.014 0.0101 0.00731 ... 
Negative eigenvalues: -0.00324 -0.0021 -0.0016 -0.00143 -0.000756 ... 

vector length mode content 
1 $eig 39 numeric eigenvalues 

data.frame nrow ncol content 
1 $c1 79 7 principal axes: scaled vectors of alleles loadings 
2 $li 118 7 principal components: coordinates of entities ('scores') 
3 $ls 118 7 lag vector of principal components 
4 $as 2 7 pca axes onto spca axes 

$xy: matrix of spatial coordinates 
$lw: a list of spatial weights (class 'listw') 

other elements: NULL 
> plot(atm1.spca.2) 
Error in data.frame(eig = eig, var = varspa, moran = moran/varspa) : 
arguments imply differing number of rows: 39, 38 
In addition: Warning message: 
In multispati(dudi = dudi, listw = lw, scannf = FALSE, nfposi = nfposimax, : 
There are only 21 positive factors. 
> 

Cheers, 
Chad 

-- 
Chad Smith 
Postdoctoral Fellow 
Dept of Integrative Biology 
University of Texas at Austin 
1 University Station C0990 
Austin, TX 78712 

Office: PAT 632 
Phone: 512-471-7619 
Fax: 512-471-3878 
https://chadcsmith.wordpress.com/ 

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From thibautjombart at gmail.com  Tue Jan 31 12:09:33 2017
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Tue, 31 Jan 2017 11:09:33 +0000
Subject: [adegenet-forum] Error in using adegenetServer(what = "DAPC")
In-Reply-To: <CANpTdqW0Ofi7_f=jr9t=eohP4ikz9urJLn6m0d4FxsRBQKy+rg@mail.gmail.com>
References: <CANpTdqW0Ofi7_f=jr9t=eohP4ikz9urJLn6m0d4FxsRBQKy+rg@mail.gmail.com>
Message-ID: <CANPRA+rDuLCuEAC0b1D0WMXq-3YsK7MTHD3eZboq+tbcO1bWYw@mail.gmail.com>

Hi there,

sorry but there is not much we can do without more details and a
reproducible example. Please file an issue on github with necessary
information for us to help.

Best
Thibaut


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

On 24 January 2017 at 05:40, Ramendra Nath Sarma <rnsarma at aau.ac.in> wrote:

> When I am loading my csv file, I have seen an message without any output
> that "unable to find an inherited method for function ?tab? for signature
> ?"NULL"?.
>
> --
> ------------------------------------------------------------
> ------------------------------------------------------------
> ----------------
>
>
>
>
>
>
> *Dr R N SarmaProfessorDepartment of Plant Breeding and GeneticsAssam
> Agricultural UniversityJorhat-785013Assam, Indiaweb: www.aau.ac.in;
> <http://www.aaau.ac.in> Phone: +91-376-2310526 <+91%20376%20231%200526>;
> +91-376231133(R); 9435350529(M)*
> ------------------------------------------------------------
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