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Thread: ADMIXTOOLS directly from R : bodkan/admixr

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    ADMIXTOOLS directly from R : bodkan/admixr

    Github https://rdrr.io/github/bodkan/admixr/
    tutorial https://bodkan.net/admixr/articles/tutorial.html

    academic paper https://academic.oup.com/bioinformat...7/3194/5298728

    Introduction

    ADMIXTOOLS is a widely used software package for calculating admixture statistics and testing population admixture hypotheses.

    A typical ADMIXTOOLS workflow generally involves a combination of sed/awk/shell scripting and manual editing to create text configuration files. These are then passed as command-line arguments to one of ADMIXTOOLS commands, and control how to run a particular analysis. The results are then redirected to another file, which has to be parsed by the user to extract values of interest, often using command-line utilities again or (worse) by manual copy-pasting. Finally, the processed results are analysed in R, Excel or another program.

    This workflow can be a little cumbersome, especially if one wants to explore many hypotheses involving different combinations of populations. Most importantly, however, it makes it difficult to coduct reproducible research, as it is nearly impossible to construct fully automated “pipelines” that don’t require user intervention.

    This R package makes it possible to perform all stages of ADMIXTOOLS analyses entirely from R, completely removing the need for “low level” configuration of individual ADMIXTOOLS programs

    Philosophy of admixr

    The goal of admixr is to make ADMIXTOOLS analyses as trivial to run as possible, without having to worry about par/pop/left/right configuration files (as they are known in the jargon of ADMIXTOOLS) and other low-level details.

    The only interface between you and ADMIXTOOLS is the following set of R functions:

    d()
    f4()
    f4ratio()
    f3()
    qpAdm()
    qpWave()

    Anything that would normally require dozens of lines of shell scripts can be often accomplished by running a single line of R code.

    Last edited by polishguy; 06-17-2020 at 09:54 AM.

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    It is not only easier to use but also functionally equal to admix tools we use on Linux, isn't it?

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    Quote Originally Posted by Kaspias View Post
    It is not only easier to use but also functionally equal to admix tools we use on Linux, isn't it?
    Author stated it. It is only runner which simplifies whole boring technical, manual stuff. It works using existing Admixtools installation, so you will get the same results / output as traditionally, but much faster. Here is the clue.

    Still needs some knowledge to install Admixtools and R on Ubuntu but then voila.

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    Falkland Bouvet Heard Island and McDonald French Southern and Antarctic Lands South Georgia and South Sandwich
    Small tip. I figured it out by myself. To force R to has in Path admixtools binaries. It is not in manual.

    Add it to .Renviron file which is (or it is in my case) located in your home ubuntu directory (select hidden files). At the end of the PATH=

    :/home/user/Desktop/AdmixTools-master/bin

    I had it on Desktop, so hence the path in my case. Your could be different.
    Last edited by polishguy; 06-17-2020 at 11:54 AM.

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    If I'm well understanding, one can use this package even if R is installed on a Windows interface, just need to have the admixtools binaries in the right folder. In this case, I doubt it will run much faster than directly on a Linux environment. If I happen to be wrong it will be good news for all people who dream to use admixtools but don't want to install a Linux. I seem to remember that a function in this package allows to merge eigenstrat files. Merging such files directly with mergeit gives, at least in my remote memories, weird results. Same remark: if that actually works fine, it will be a pretty nice event. Honestly I'll not try it myself, as I have too long habits with Linux to change anything to them, but I'm curious.

    Without rapport: Kaspias I find your avatar picture magnificent. Where does it come from?
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    Falkland Bouvet Heard Island and McDonald French Southern and Antarctic Lands South Georgia and South Sandwich
    Quote Originally Posted by anglesqueville View Post
    If I'm well understanding, one can use this package even if R is installed on a Windows interface, just need to have the admixtools binaries in the right folder. In this case, I doubt it will run much faster than directly on a Linux environment. If I happen to be wrong it will be good news for all people who dream to use admixtools but don't want to install a Linux. I seem to remember that a function in this package allows to merge eigenstrat files. Merging such files directly with mergeit gives, at least in my remote memories, weird results. Same remark: if that actually works fine, it will be a pretty nice event. Honestly I'll not try it myself, as I have too long habits with Linux to change anything to them, but I'm curious.
    I don't even think about possibility of using it in Windows, maybe you are right and it could be used there too.
    In Ubuntu admixr is very fast.

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    Quote Originally Posted by polishguy View Post
    I don't even think about possibility of using it in Windows, maybe you are right and it could be used there too.
    In Ubuntu admixr is very fast.
    I'm sure that some anti-Linux guy will try. We'll see.
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    Quote Originally Posted by anglesqueville View Post
    If I'm well understanding, one can use this package even if R is installed on a Windows interface, just need to have the admixtools binaries in the right folder. In this case, I doubt it will run much faster than directly on a Linux environment. If I happen to be wrong it will be good news for all people who dream to use admixtools but don't want to install a Linux. I seem to remember that a function in this package allows to merge eigenstrat files. Merging such files directly with mergeit gives, at least in my remote memories, weird results. Same remark: if that actually works fine, it will be a pretty nice event. Honestly I'll not try it myself, as I have too long habits with Linux to change anything to them, but I'm curious.

    Without rapport: Kaspias I find your avatar picture magnificent. Where does it come from?
    Is it possible to find admixtools binaries somewhere on the web for download

    It says: "The software runs on Linux and macOS and these are the two systems that admixr is tested on."

    I doubt that it could work properly on Windows.
     
    All simple calculations, maps and plots I make for free, but for more complicated maps and calculations I ask for a donation via Hidden Content PayPalHidden Content account

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    Falkland Bouvet Heard Island and McDonald French Southern and Antarctic Lands South Georgia and South Sandwich
    Quote Originally Posted by ph2ter View Post
    Is it possible to find admixtools binaries somewhere on the web for download
    Bin folder in Admixtools appears after proper installation apparently. In downloaded version I don't see it.

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    Quote Originally Posted by anglesqueville View Post
    Without rapport: Kaspias I find your avatar picture magnificent. Where does it come from?
    It is a representation of Turkic woman from the "Brides of Silk Road" art collection by Tang Wei Min.

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