[adegenet-forum] problems with na.replace and values for n.pca & n.da
D. Magdalena Sorger
dm.sorger at gmail.com
Mon Oct 19 22:55:16 CEST 2015
Hi Roman (and everyone else),
Thank you, it looks like this is the same tutorial I had been using and
that my questions refer to (July 29, 2015).
Please, let me know if anyone can help me with my questions, both regarding
replacing missing allele data but also (and more importantly) regarding the
selection of the # of PCs and the # of discriminant functions (see below).
Best,
Magdalena
On Fri, Oct 16, 2015 at 10:32 AM, Roman Lustrik <roman.lustrik at biolitika.si>
wrote:
> Hello Magdalena,
>
> you can find a DAPC tutorial on GitHub:
> https://github.com/thibautjombart/adegenet/wiki/Tutorials
>
> HTH,
> Roman
>
>
> ----
> In god we trust, all others bring data.
>
> ------------------------------
> *From: *"D. Magdalena Sorger" <dm.sorger at gmail.com>
> *To: *"Thibaut Jombart" <t.jombart at imperial.ac.uk>
> *Cc: *adegenet-forum at lists.r-forge.r-project.org
> *Sent: *Thursday, October 15, 2015 7:45:18 PM
>
> *Subject: *Re: [adegenet-forum] problems with na.replace and values for
> n.pca & n.da
>
> Dear Thibaut,
>
> I found the information on scaleGen() in a tutorial from July 29, 2015 on
> the adegenet website:
> http://adegenet.r-forge.r-project.org/files/tutorial-basics.pdf
>
> Other than this function, I didn't find any instructions on how to treat
> missing values in that tutorial. I also didn't find instructions for how to
> use tab() to replace missing values.
>
> If I just read my raw data in (missing allele values denoted as "NA" in
> genepop file), it informs me that there is 0% missing data which is what
> concerns me:
>
> *> msts_m2<-read.genepop("BOR-Od_m2_301w.gen") *
> *> summary(msts_m2)*
>
> *// Number of individuals: 301*
> *// Group sizes: 12 9 18 12 20 11 18 18 12 12 17 18 20 28 12 12 12 11 12
> 17*
> *// Number of alleles per locus: 4 4 13 19 20 10 20 7*
> *// Number of alleles per group: 16 17 18 18 26 18 23 21 18 19 22 17 17 31
> 19 16 21 17 18 16*
> *// Percentage of missing data: 0 %*
> *// Observed heterozygosity: 0.41 0.55 0.81 0.66 0.79 0.69 0.78 0.74*
> *// Expected heterozygosity: 0.39 0.6 0.88 0.87 0.92 0.75 0.92 0.76*
> *> *
>
>
>
> When I call tab, it lists the missing data at e.g., locus loc21 as
> loc21.NA:
>
> > msts_m2[loc="loc21"]@tab
> loc21.02 loc21.03 loc21.NA loc21.04 loc21.05 loc21.06 loc21.01
> 1 1 1 0 0 0 0 0
> 2 2 0 0 0 0 0 0
> 3 2 0 0 0 0 0 0
> 4 1 1 0 0 0 0 0
> 5 1 1 0 0 0 0 0
>
>
>
> I also tried this, but the output remains the same as above:
>
>
> *tab(msts_m2, missing="mean")*
>
>
>
> Best,
> Magdalena
>
>
> On Thu, Oct 15, 2015 at 9:10 AM, Jombart, Thibaut <
> t.jombart at imperial.ac.uk> wrote:
>
>> Hi there,
>>
>> please check the current tutorials. scaleGen is no longer used, and has
>> been replaced by tab. Then you should be able to feed the resulting object
>> to dapc without problem.
>>
>> Cheers
>> Thibaut
>>
>>
>>
>> ------------------------------
>> *From:* D. Magdalena Sorger [dm.sorger at gmail.com]
>> *Sent:* 15 October 2015 02:36
>> *To:* Jombart, Thibaut
>> *Cc:* adegenet-forum at lists.r-forge.r-project.org
>> *Subject:* Re: [adegenet-forum] problems with na.replace and values for
>> n.pca & n.da
>>
>> Dear all,
>>
>> I updated my adegenet package, however, I still have issues with
>> confirming that it is reading my missing values in correctly.
>>
>> I now use this code to read in my genepop file:
>> *msts_m2<-read.genepop("BOR-Od_m2_301w.gen") *
>>
>> I tried this line of code for replacing NA's with means:
>> *msts_m2 <- scaleGen(msts_m2, NA.method="mean")*
>>
>> ....but this just seems to be appropriate for the regular PCA and my DAPC
>> code (see below) won't work and give me this error: Error in (function
>> (classes, fdef, mtable): unable to find an inherited method for function
>> ‘pop’ for signature ‘"matrix"’
>>
>> Therefore: What is the proper way to treat missing values (denoted as NA
>> in my genepop file) for a DAPC - do they need to be replaced with means
>> (which I assume) and if so what is the proper line of code to do that?
>>
>> If I don't run the scaleGen line of code and continue with the DAPC code
>> (see below), I still get the same output I had questions about earlier (see
>> below).
>>
>> Best,
>> Magdalena
>>
>>
>>
>>
>> On Mon, Oct 12, 2015 at 6:21 AM, Jombart, Thibaut <
>> t.jombart at imperial.ac.uk> wrote:
>>
>>> Hi there,
>>>
>>> your post suggests you are using an outdated version of adegenet -
>>> na.replace and some arguments you are using have been removed from the
>>> package since version 2.0.0. This means you have been consulting an
>>> outdated version of the tutorials.. where did you find it? If there is
>>> outdated doc around I need to get rid of it.
>>>
>>> Please update to the devel version (2.0.1) from github:
>>> https://github.com/thibautjombart/adegenet
>>>
>>> Current tutorials should answer your first question. Missing data are
>>> detected automatically if the right format is used. Let's wait to make sure
>>> your data were imported fine for the others.
>>>
>>> Cheers
>>> Thibaut
>>>
>>> ==============================
>>> Dr Thibaut Jombart
>>> MRC Centre for Outbreak Analysis and Modelling
>>> Department of Infectious Disease Epidemiology
>>> Imperial College - School of Public Health
>>> Norfolk Place, London W2 1PG, UK
>>> Tel. : 0044 (0)20 7594 3658
>>> http://sites.google.com/site/thibautjombart/
>>> http://sites.google.com/site/therepiproject/
>>> http://adegenet.r-forge.r-project.org/
>>> Twitter: @thibautjombart
>>>
>>>
>>> ------------------------------
>>> *From:* adegenet-forum-bounces at lists.r-forge.r-project.org [
>>> adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of D.
>>> Magdalena Sorger [dm.sorger at gmail.com]
>>> *Sent:* 09 October 2015 20:00
>>> *To:* adegenet-forum at lists.r-forge.r-project.org
>>> *Subject:* [adegenet-forum] problems with na.replace and values for
>>> n.pca & n.da
>>>
>>> Dear all,
>>>
>>> I am trying to constuct a DAPC scatterplot with adegenet and have three
>>> questions that after consulting online resources, tutorials, etc. still
>>> haven't been answered definitively.
>>>
>>>
>>> My data set consists of (diploid) microsatellite data (8 markers) for 20
>>> ant colonies of 9-28 workers each (mean=15), 301 workers total. I have
>>> missing data in 7 spots (i.e. individuals with missing data at one or more
>>> loci). My first question is about reading in the genepop file:
>>>
>>> *1) What is the proper command for reading in my file in regards to
>>> missing data? *
>>>
>>> I had replaced all missing data ("0000") with "NA" in the genepop file
>>> and used the below code assuming that it would recognize my missing data as
>>> NA (first line of code) and replace missing values with means (second line):
>>>
>>>
>>> *msts_m2<-read.genepop("BOR-Od_m2_301w.gen",missing="NA")
>>> na.replace(msts_m2,"mean", quiet=FALSE)*
>>>
>>> However, when I run this code, it informs me that it replaced 119
>>> missing values. This obviously seems too much as it should have only
>>> replaced 7. I'm not sure why this isn't working, see output below
>>>
>>>
>>> *OUTPUT:*
>>> *> na.replace(msts_m2,"mean", quiet=FALSE) *
>>>
>>> * Replaced 119 missing values *
>>>
>>> * #####################*
>>> * ### Genind object ### *
>>> * #####################*
>>> *- genotypes of individuals - *
>>>
>>> *S4 class: genind*
>>> *@call: read.genepop(file = "BOR-Od_m2_301w.gen", missing = "NA")*
>>>
>>> *@tab: 301 x 93 matrix of genotypes*
>>>
>>> *@ind.names: vector of 301 individual names*
>>> *@loc.names: vector of 8 locus names*
>>> *@loc.nall: number of alleles per locus*
>>> *@loc.fac: locus factor for the 93 columns of @tab*
>>> *@all.names: list of 8 components yielding allele names for each locus*
>>> *@ploidy: 2*
>>> *@type: codom*
>>>
>>> *Optionnal contents: *
>>> *@pop: factor giving the population of each individual*
>>> *@pop.names: factor giving the population of each individual*
>>>
>>> *@other: - empty -*
>>>
>>>
>>>
>>>
>>>
>>> My second and third questions relate to the selection of the # of PCs
>>> and the # of discriminant functions to retain. It seems that each time I
>>> make slight changes to these numbers, the output changes vastly and so I
>>> want to make sure I input the proper numbers.
>>>
>>> First I use the find.clusters function, I designate 20 for n.pca here
>>> since I have 20 colonies:
>>>
>>> *clusters<-find.clusters(msts_m2,max.n.pca=20)*
>>>
>>> When asked for the number of PCs to retain I select 30 which is the
>>> level at which the points seem to level off. The BIC graph looks nothing
>>> like the graph in the vignette (it does not level off but below a certain
>>> level shows a downward zigzag pattern) so I choose 20 given that I have 20
>>> colonies.
>>>
>>> *dapc_m2<-dapc(msts_m2,clusters$grp)*
>>> [image: Inline image 1][image: Inline image 2]
>>> Next, when asked for PCs to retain I again choose the level at which the
>>> points start to level off (30) but when asked for discriminant functions to
>>> retain, I'm at a loss. I have about 18 relatively constantly decreasing
>>> bars. I usually choose the point between the first few ones and the rest
>>> where there is some kind of bigger (sometimes arbitrary) break and use that
>>> number (in this case: 4):
>>>
>>> *2) How to choose the appropriate number for PCs to retain and discr.
>>> functions to retain?*
>>>
>>>
>>> *[image: Inline image 3][image: Inline image 4] *
>>>
>>>
>>>
>>> *best.n.pca<-a.score(dapc_m2)*
>>> *temp<-optim.a.score(dapc_m2)*
>>>
>>> After running the optim.a.score function I receive a graph that tells me
>>> at the top "optimal number of PCs". This is the number I put into my last
>>> line of code (below) for n.pca, and for n.da I choose the number I used
>>> when prompted earlier:
>>>
>>> *3) Are these the correct numbers to use for this last line of code? *
>>>
>>> *dapc_m2<-dapc(msts_m2,n.pca=7,n.da=4)*
>>>
>>>
>>>
>>> --
>>> Magdalena Sorger
>>> ____________
>>> Department of Applied Ecology
>>> North Carolina State University
>>> 127 David Clark Labs, Box 7617
>>> 100 Eugene Brooks Ave.
>>> Raleigh, NC 27695, USA
>>> # 919-513-7464
>>> dmsorger at ncsu.edu
>>> *www.theantlife.com* <http://www.theantlife.com>
>>>
>>
>>
>>
>> --
>> Magdalena Sorger
>> ____________
>> Department of Applied Ecology
>> North Carolina State University
>> 127 David Clark Labs, Box 7617
>> 100 Eugene Brooks Ave.
>> Raleigh, NC 27695, USA
>> # 919-513-7464
>> dmsorger at ncsu.edu
>> *www.theantlife.com* <http://www.theantlife.com>
>>
>
>
>
> --
> Magdalena Sorger
> ____________
> Department of Applied Ecology
> North Carolina State University
> 127 David Clark Labs, Box 7617
> 100 Eugene Brooks Ave.
> Raleigh, NC 27695, USA
> # 919-513-7464
> dmsorger at ncsu.edu
> *www.theantlife.com* <http://www.theantlife.com>
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
>
>
--
Magdalena Sorger
____________
Department of Applied Ecology
North Carolina State University
127 David Clark Labs, Box 7617
100 Eugene Brooks Ave.
Raleigh, NC 27695, USA
# 919-513-7464
dmsorger at ncsu.edu
*www.theantlife.com* <http://www.theantlife.com>
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