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
sed/awk/shell 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!
To install admixr from Github you need to install the
package devtools first. You can simply run:
install.packages("devtools")
devtools::install_github("bodkan/admixr")If you want to update admixr to a more
recent version, simply run
devtools::install_github("bodkan/admixr") again.
Note that in order to use the admixr package,
you need a working installation of ADMIXTOOLS! You can find
installation instructions here.
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 prefix here.
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 487646Note 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.