From postmaster at r-forge.wu-wien.ac.at  Mon Feb  1 11:55:07 2016
From: postmaster at r-forge.wu-wien.ac.at (The Post Office)
Date: Mon, 1 Feb 2016 13:55:07 +0300
Subject: [adegenet-forum] Delivery reports about your e-mail
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From postmaster at r-forge.wu-wien.ac.at  Wed Feb 10 15:25:05 2016
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From goatsrunfaster at gmail.com  Tue Feb 23 23:20:38 2016
From: goatsrunfaster at gmail.com (Spencer Bruce)
Date: Tue, 23 Feb 2016 17:20:38 -0500
Subject: [adegenet-forum] PCA for microsat data
Message-ID: <CAGjKGeb+e6_=N-tNiCaFW_bT8tUj6DjnGQKahgNcc8zP_abtdA@mail.gmail.com>

I've done everything in the DAPC tutorial using this data set over and over
no problem, but now I'm attempting to do a simple PCA and I seem to keep
running into problems with my genind object.

I'm sure ill get some backlash for being a self-taught beginner here, but
any help is really greatly appreciated.

I've imported my STRUCTURE file as a Gendind object no problem.
Right off the bat its as if adgenet does not recognize the data in the
object, see object and following code below...

>fish
  #####################
   ### Genind object ###
   #####################
- genotypes of individuals -

S4 class:  genind
@call: read.structure(file = file, missing = missing, quiet = quiet)

@tab:  391 x 172 matrix of genotypes

@ind.names: vector of  391 individual names
@loc.names: vector of  11 locus names
@loc.nall: number of alleles per locus
@loc.fac: locus factor for the  172 columns of @tab
@all.names: list of  11 components yielding allele names for each locus
@ploidy:  2
@type:  codom

Optional contents:
@pop:  factor giving the population of each individual
@pop.names:  factor giving the population of each individual

@other: - empty -

> data(fish)
Warning message:
In data(fish) : data set ?fish? not found
> sum(is.na(fish$tab))
[1] 166
> X <- scaleGen(fish, NA.method="mean")
Error in .local(x, ...) : unused argument (NA.method = "mean")
> class(X)
Error: object 'X' not found

I also tried this:
> X <- scaleGen(fish$tab, NA.method="mean")
Error in (function (classes, fdef, mtable)  : unable to find an inherited
method for function ?scaleGen? for signature ?"matrix"?

Am i missing something wildly simple here? Any help is greatly greatly
appreciated...
-- 
Spencer A Bruce
113 Hill St.
Troy, NY 12180
518 225 0787
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From roman.lustrik at biolitika.si  Wed Feb 24 08:50:49 2016
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Wed, 24 Feb 2016 08:50:49 +0100 (CET)
Subject: [adegenet-forum] PCA for microsat data
In-Reply-To: <CAGjKGeb+e6_=N-tNiCaFW_bT8tUj6DjnGQKahgNcc8zP_abtdA@mail.gmail.com>
References: <CAGjKGeb+e6_=N-tNiCaFW_bT8tUj6DjnGQKahgNcc8zP_abtdA@mail.gmail.com>
Message-ID: <995646431.1367366.1456300249512.JavaMail.zimbra@biolitika.si>

Hi, 

the `data(fish)` won't work because this is a command that fetches a dataset that is shipped with R or a package. 

As for the rest of the errors, can you type `traceback()` after an error and send us the output? Or ideally, if you are allowed to share the dataset, that would be great so that it can be debugged directly. 

Cheers, 
Roman 

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

----- Original Message -----

From: "Spencer Bruce" <goatsrunfaster at gmail.com> 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Tuesday, February 23, 2016 11:20:38 PM 
Subject: [adegenet-forum] PCA for microsat data 

I've done everything in the DAPC tutorial using this data set over and over no problem, but now I'm attempting to do a simple PCA and I seem to keep running into problems with my genind object. 

I'm sure ill get some backlash for being a self-taught beginner here, but any help is really greatly appreciated. 

I've imported my STRUCTURE file as a Gendind object no problem. 
Right off the bat its as if adgenet does not recognize the data in the object, see object and following code below... 

>fish 
##################### 
### Genind object ### 
##################### 
- genotypes of individuals - 

S4 class: genind 
@call: read.structure(file = file, missing = missing, quiet = quiet) 

@tab: 391 x 172 matrix of genotypes 

@ind.names: vector of 391 individual names 
@loc.names: vector of 11 locus names 
@loc.nall: number of alleles per locus 
@loc.fac: locus factor for the 172 columns of @tab 
@all.names: list of 11 components yielding allele names for each locus 
@ploidy: 2 
@type: codom 

Optional contents: 
@pop: factor giving the population of each individual 
@pop.names: factor giving the population of each individual 

@other: - empty - 

> data(fish) 
Warning message: 
In data(fish) : data set ?fish? not found 
> sum( is.na (fish$tab)) 
[1] 166 
> X <- scaleGen(fish, NA.method="mean") 
Error in .local(x, ...) : unused argument (NA.method = "mean") 
> class(X) 
Error: object 'X' not found 

I also tried this: 
> X <- scaleGen(fish$tab, NA.method="mean") 
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ?scaleGen? for signature ?"matrix"? 

Am i missing something wildly simple here? Any help is greatly greatly appreciated... 
-- 
Spencer A Bruce 
113 Hill St. 
Troy, NY 12180 
518 225 0787 

_______________________________________________ 
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 17869067 at students.latrobe.edu.au  Mon Feb 29 20:19:10 2016
From: 17869067 at students.latrobe.edu.au (LAURA NICOLE WOODINGS)
Date: Mon, 29 Feb 2016 19:19:10 +0000
Subject: [adegenet-forum] Different versions giving different results
Message-ID: <D2FAE4DE.ADD3%17869067@students.latrobe.edu.au>

Hi,

I am using DAPC to find genetic clusters within my data. The problem I am having is that I was using an older version (I'm not sure what version) of adegenet to do the analysis and I have upgraded to version 2.0.1. I wanted to rerun a DAPC and it wouldn't work with commands and the files that had been created and worked in the older version (I suspect this was because I had used na.replace to replace missing data values). I have now got the data to work by replacing the missing data with  tab(pop1to3_bp75_cnt100_cl98, NA.method="zero") but the results I am getting for group assignment in the new version (Cluster 1: 20, Cluster 2: 67) are different to what I was getting before (Cluster 1: 84, Cluster 2: 4) . I don't think that the missing data is being replaced properly in my read.structure file. Also the tab() command turns the file from a genind object to a data frame, is that meant to happen?
Below are my commands for the old version and v2.0.1 :

Old version commands

pop1to3_bp75_cnt75_cl96 <- read.structure("../noreps_pop1to3_neutral_75bp_cnt75_cl96_2-16_ml80._maf0.10_missing0.8_hwe0.001.stru", n.ind=87, n.loc=813, onerowperind=TRUE, col.lab=1, col.pop=2, row.marknames=1)
summary(pop1to3_bp75_cnt75_cl96)
# Percentage of missing data:
[1] 5.308846
sum(is.na(pop1to3_bp75_cnt75_cl96$tab))
[1] 7510
pop1to3_bp75_cnt75_cl96NoNA <- na.replace(pop1to3_bp75_cnt75_cl96,"0")
  Replaced 7510 missing values
pop1to3_757596clust<- find.clusters(pop1to3_bp75_cnt75_cl96NoNA)
Choose the number PCs to retain (>=1):
  110
Choose the number of clusters (>=2:
                                 2
pop1to3_dapc_bp75_cnt75_cl96 <- dapc(pop1to3_bp75_cnt75_cl96NoNA, pop=pop1to3_757596clust$grp)
    Choose the number PCs to retain (>=1):
    25
   Choose the number discriminant functions to retain (>=1):
    1
assignplot(pop1to3_dapc_bp75_cnt75_cl96)

2.0.1 verion commands:
pop1to3_bp757596 <- read.structure("../noreps_pop1to3_neutral_75bp_cnt75_cl96_2-16_ml80._maf0.10_missing0.8_hwe0.001.stru", n.ind=87, n.loc=813, onerowperind=TRUE, col.lab=1, col.pop=2, row.marknames=1, NA.char=0) #doesn't read missing data without NA.char specified
summary_75_100_98 <- summary(pop1to3_bp757596)
# Percentage of missing data:
[1] 5.308846
sum(is.na(tab(pop1to3_bp757596)))
[1] 7514
pop1to3_bp757596NoNA <- tab(pop1to3_bp757596, NA.method="zero")
pop1to3_757596clust_2nd<- find.clusters(pop1to3_bp757596NoNA)
Choose the number PCs to retain (>=1):
  100
Choose the number of clusters (>=2:
  2
pop1to3_dapc_bp757596<- dapc(pop1to3_bp757596NoNA, grp=pop1to3_757596clust_2nd)
Choose the number PCs to retain (>=1):
                                 25
Choose the number discriminant functions to retain (>=1):
                                 1
assignplot(pop1to3_dapc_bp757596)

Any help would be greatly appreciated.

Thanks
Laura
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From kimash21 at gmail.com  Wed Feb 10 22:18:43 2016
From: kimash21 at gmail.com (Kimani Kitson-Walters)
Date: Wed, 10 Feb 2016 21:18:43 -0000
Subject: [adegenet-forum] Warning Messages when plotting spca and editing
	Connection Networks
Message-ID: <CAP38GpFAqF1B3ybLV4bYUxW602TeD1u7Oss2aZ-FYfbKCfoEEg@mail.gmail.com>

Hello All,

I'm pretty new to R and this forum. I've spent the last 2 days searching
through the archive but to no avail.

I've run an spca on my data which includes 5 populations with fragment
sizes for 9 microsatellite loci. Each population has between 22 and 39
individuals. The xy coordinates for the 5 populations has been loaded to
the "other" slot the genepop file containing my data. I however keep
getting warning messages and I haven't been able to figure out why. I've
been trying to wrap my head around statistics and R for a while now and I'm
making some improvements but this one has me stumped. There are two issues:

1. I'm trying to edit the connection network using edit.nb but R keeps
aborting and restarts the session when I begin to interact with the graph
to select the connection I want to delete.

spca<- spca(obj, edit.nb=TRUE)

2.The spca runs without a hitch when I use spca(). The problem is that I
get the warning messages when I plot it using plot (spca). I have also run
the Global and Local tests as well before I plot the spca the result.
Below is the script I use and the resulting errors:

> spca <- spca(obj)

Choose a connection network:
Delaunay triangulation (type 1)
Gabriel graph (type 2)
Relative neighbours (type 3)
Minimum spanning tree (type 4)
Neighbourhood by distance (type 5)
K nearest neighbours (type 6)
Inverse distances (type 7)
Answer:
2 - Gabriel graph

Keep this graph (y/n)?
y
Select the first number of axes (>=1):
1
Select the second number of axes (>=0):
2

[image: pasted1]

> X<- scaleGen(obj)###Gets rid of missing data
>
> myGtest <- global.rtest(X,spca$lw,nperm=50000)###Runs global stats
> myGtest
Monte-Carlo test
Call: global.rtest(X = X, listw = spca$lw, nperm = 50000)

Observation: 0.2588172

Based on 50000 replicates
Simulated p-value: 0.647667
Alternative hypothesis: greater

     Std.Obs  Expectation     Variance
-0.445824651  0.266881510  0.000327198
> plot(myGtest)
> myLtest <- local.rtest(X,spca$lw,nperm=50000)###Runs local Stats
> myLtest
Monte-Carlo test
Call: local.rtest(X = X, listw = spca$lw, nperm = 50000)

Observation: 0.2573817

Based on 50000 replicates
Simulated p-value: 0.7091858
Alternative hypothesis: greater

      Std.Obs   Expectation      Variance
-0.6498182785  0.2675756071  0.0002460908

plot(spca)
[image: pasted2]
Warning messages:
1: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
 :
  span too small.   fewer data values than degrees of freedom.
2: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
 :
  pseudoinverse used at -151.9 50.468
3: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
 :
  neighborhood radius 3.8482
4: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
 :
  reciprocal condition number  0
5: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
 :
  There are other near singularities as well. 14.477
6: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
 :
  Chernobyl! trL>n 3.5458
7: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
 :
  Chernobyl! trL>n 3.5458

I hope you'll be able to help me or direct me to some help. I'm a strict
biologist and this is my first plunge into spatial genetic analysis.

Thanks
-- 


Mr. Kimani Kitson-Walters BSc (Hons)
Smithsonian Link Fellow 2015
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From nina.marchi at mnhn.fr  Fri Feb 12 20:08:22 2016
From: nina.marchi at mnhn.fr (Nina Marchi)
Date: Fri, 12 Feb 2016 19:08:22 -0000
Subject: [adegenet-forum] Help for running fst on genlight data
Message-ID: <B0B82E10-FC0D-4B72-B062-BEC46A51B285@mnhn.fr>

Good evening,

I am trying to run Fst distances on a SNP data set (200 000 SNPs in a Plink file). I am using adegenet 2.0.0 and I have imported the data as a genlight "table". But I did not found a way to calculate a Fst from this format. Can you please tell me a way to do it with adegenet ? I have to use the genlight format as my data are under a plink format. Do I have to convert the genlight as genind (but how?) ?

Thank you very much

Nina Marchi
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