ADMIXTOOLS is a widely used software package for calculating admixture statistics and testing population admixture hypotheses.
A typical ADMIXTOOLS workflow often involves a combination of
scripting and manual editing to create different 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 follow the rules of best practice for reproducible science, as it is nearly impossible to construct reproducible automated "pipelines".
This R package makes it possible to perform all stages of an ADMIXTOOLS analysis entirely from R. It provides a set of convenient functions that completely remove the need for "low level" configuration of individual ADMIXTOOLS programs, allowing users to focus on the analysis itself.
admixr is now published as an Application Note in the journal Bioinformatics. If you use it in your work, please cite the paper!
admixr from Github you need to install the package
first. You can simply run:
If you want to update admixr to a more recent version, simply
Note that in order to use the
admixr package, you need a working
installation of ADMIXTOOLS! You can find installation instructions
Furthermore, you need to make sure that R can find ADMIXTOOLS binaries on the
$PATH. If this is not the case, running
library(admixr) will show a
warning message with instructions on how to fix this.
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This is all the code that you need to perform ADMIXTOOLS analyses using this
package! No shell scripting, no copy-pasting and manual editing of text files.
The only thing you need is a working ADMIXTOOLS installation and a path to
EIGENSTRAT data (a trio of ind/snp/geno files), which we call
library(admixr) # download a small testing dataset to a temporary directory and # process it for use in R snp_data <- eigenstrat(download_data()) result <- d( W = c("French", "Sardinian"), X = "Yoruba", Y = "Vindija", Z = "Chimp", data = snp_data ) result #> # A tibble: 2 x 10 #> W X Y Z D stderr Zscore BABA ABBA nsnps #> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 French Yoruba Vindija Chimp 0.0313 0.00693 4.51 15802 14844 487753 #> 2 Sardinian Yoruba Vindija Chimp 0.0287 0.00679 4.22 15729 14852 487646
Note that a single call to the
d function generates all required intermediate
config and population files, runs ADMIXTOOLS, parses its log output and returns
the result as a
data.frame object. It does all of this behind the scenes,
without the user having to deal with low-level technical details.
To see many more examples, please check out the tutorial vignette.
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