AMOVA with Structure file
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Ramendra Sarma
Nov 5, 2015, 9:56:02 AM11/5/15
to poppr
Hio,
What steps should I follow to AMOVA with a file formated for Structure? Sorry for a simple quiestion since I am new to to poppr
Zhian Kamvar
Nov 5, 2015, 10:03:24 AM11/5/15
to Ramendra Sarma, poppr
Hello,
You can find out how to import data with adegenet's "basics" tutorial located here: https://github.com/thibautjombart/adegenet/blob/master/tutorials/tutorial-basics.pdf
From there, your STRUCTURE file should import as a genind object. If you want to use population strata in your AMOVA analysis, you should read the "strata" tutorial: https://github.com/thibautjombart/adegenet/blob/master/tutorials/tutorial-strata.pdf
After that, you can perform amova with the function poppr.amova. For details, see the help page for the function by typing help("poppr.amova") in your R console.
Best,
Zhian
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You can find out how to import data with adegenet's "basics" tutorial located here: https://github.com/thibautjombart/adegenet/blob/master/tutorials/tutorial-basics.pdf
From there, your STRUCTURE file should import as a genind object. If you want to use population strata in your AMOVA analysis, you should read the "strata" tutorial: https://github.com/thibautjombart/adegenet/blob/master/tutorials/tutorial-strata.pdf
After that, you can perform amova with the function poppr.amova. For details, see the help page for the function by typing help("poppr.amova") in your R console.
Best,
Zhian
> On Nov 5, 2015, at 02:45 , Ramendra Sarma <ramendr...@gmail.com> wrote:
>
>
>
> Hio,
> What steps should I follow to AMOVA with a file formated for Structure? Sorry for a simple quiestion since I am new to to poppr
>
> --
>
>
>
> Hio,
> What steps should I follow to AMOVA with a file formated for Structure? Sorry for a simple quiestion since I am new to to poppr
>
> You received this message because you are subscribed to the Google Groups "poppr" group.
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Ramendra Sarma
Nov 7, 2015, 11:21:43 AM11/7/15
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Being novice to R, I ma finding it difficult perform 'poppr.amova' with my data in structure format with 4 populations. The error message that Im receiving are:
amova<-read.structure(("/home/ramen/Joha_works/Structure_gui/joha_amova.str"))
How many genotypes are there?
54
How many markers are there?
88
Which column contains labels for genotypes ('0' if absent)?
1
Which column contains the population factor ('0' if absent)?
2
Which other optional columns should be read (press 'return' when done)?
1:
Which row contains the marker names ('0' if absent)?
1
Are genotypes coded by a single row (y/n)?
n
Converting data from a STRUCTURE .stru file to a genind object...
> AMOVAamova <- poppr.amova(amova,missing='ignore')
Error in poppr.amova(amova, missing = "ignore") :
A population hierarchy must be specified
> AMOVAamova <- poppr.amova(amova,missing='ignore', ~Pop/Subpop)
Error: One or more levels in the given strata is not present in the data frame.
How to resolve this issue?
amova<-read.structure(("/home/ramen/Joha_works/Structure_gui/joha_amova.str"))
How many genotypes are there?
54
How many markers are there?
88
Which column contains labels for genotypes ('0' if absent)?
1
Which column contains the population factor ('0' if absent)?
2
Which other optional columns should be read (press 'return' when done)?
1:
Which row contains the marker names ('0' if absent)?
1
Are genotypes coded by a single row (y/n)?
n
Converting data from a STRUCTURE .stru file to a genind object...
> AMOVAamova <- poppr.amova(amova,missing='ignore')
Error in poppr.amova(amova, missing = "ignore") :
A population hierarchy must be specified
> AMOVAamova <- poppr.amova(amova,missing='ignore', ~Pop/Subpop)
Error: One or more levels in the given strata is not present in the data frame.
How to resolve this issue?
Zhian Kamvar
Nov 7, 2015, 1:51:18 PM11/7/15
to Ramendra Sarma, poppr
Hi,
This error:
Error: One or more levels in the given strata is not present in the data frame.
means that you tried to specify a level of population strata that doesn't exist. You must specify your population strata in order to specify the hierarchy. Please read the tutorial on defining strata here: https://github.com/thibautjombart/adegenet/blob/master/tutorials/tutorial-strata.pdf
We also have a tutorial for performing AMOVA here: http://grunwaldlab.github.io/Population_Genetics_in_R/AMOVA.html
Best,
Zhian
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