admixr

Introduction

ADMIXTOOLS is a widely used software package for calculating admixture statistics and testing population admixture hypotheses. However, although powerful and comprehensive, it is not exactly known for being user-friendly.

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 is very 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.

Installation instructions

Note (2018/10/30): This package is currently in the last phase of testing and polishing the API before I submit it to CRAN. You can definitely safely use it for your own work, but please make sure to check back here for instructions on how to install the officially released version. You can also follow me on Twitter if you want to stay updated.

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 newer 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.

Example

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 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.