README.md

ADMIXTOOLS 2

A new, lightning fast implementation of ADMIXTOOLS.

Overview

ADMIXTOOLS is a collection of programs which use genetic data to infer how populations are related to one another. It has been used in countless publications to test whether populations form clades (qpDstat, qpWave), to estimate ancestry proportions (qpAdm), and to fit admixture graphs (qpGraph).

ADMIXTOOLS 2 provides the same functionality as ADMIXTOOLS in a new look, and it’s orders of magnitude faster. This is achieved through separating the computation of f2-statistics from all other computations, and through a number of other optimizations. In the example below, rendering the plot takes much longer than computing the fit of a new qpGraph model:

app demo

Features

Installation

ADMIXTOOLS 2 is currently still under active development. Most of it has already been tested extensively, but functionality is still added and may change here and there. ADMIXTOOLS 2 is not yet on the CRAN servers (so you can’t install it with install.packages()), but you can install it from github with the following commands (provided you have R version 3.5 or higher):

install.packages("devtools") # if "devtools" is not installed already
devtools::install_github("uqrmaie1/admixtools")
library("admixtools")

The above commands will install all R package dependencies which are required to run ADMIXTOOLS 2 on the command line. For the interactive app, additional packages are required, which can be installed like this:

devtools::install_github("uqrmaie1/admixtools", dependencies = TRUE)

If you encounter any problems during the installation, this is most likely because some of the required R packages cannot be installed. If that happens, try manually re-installing some of the larger packages, and pay attention to any error message:

install.packages("Rcpp")
install.packages("tidyverse")
install.packages("igraph")
install.packages("plotly")

Running devtools::install_github("uqrmaie1/admixtools") will compile C++ from source code (this isn’t necessary when installing packages from CRAN with install.packages()).

If you get the following error:

Error: Failed to install 'admixtools' from GitHub: Could not find tools necessary to compile a package.

you might be able to solve the problem by installing Rtools for your version of R if you use Windows, or Xcode command line tools if you use macOS. This is also described here.

If this doesn’t help, please contact me.

Usage

Admixture graphs can be fitted like this:

genotype_data = "/my/geno/prefix"
fit = qpgraph(genotype_data, example_graph)
fit$score
#> [1] 19219.98
plot_graph(fit$edges)

example graph Clearly not a historically accurate model, but it gets the idea across.

When testing more than one model, it makes sense to extract and re-use f2-statistics:

f2_blocks = f2_from_geno(genotype_data)
fit = qpgraph(f2_blocks, example_graph)
fit$score
#> [1] 19219.98

f2-statistics can also be used to estimate admixture weights:

left = c("Altai_Neanderthal.DG", "Vindija.DG")
right = c("Chimp.REF", "Mbuti.DG", "Russia_Ust_Ishim.DG", "Switzerland_Bichon.SG")
target = "Denisova.DG"
qpadm(f2_blocks, left, right, target)$weights
#> # A tibble: 2 x 5
#>   target      left                 weight    se     z
#>   <chr>       <chr>                 <dbl> <dbl> <dbl>
#> 1 Denisova.DG Altai_Neanderthal.DG   49.6  23.3  2.13
#> 2 Denisova.DG Vindija.DG            -48.6  23.3 -2.08

Or to get f4-statistics:

f4(f2_blocks)
#> # A tibble: 105 x 8
#>    pop1        pop2         pop3    pop4            est      se      z         p
#>    <chr>       <chr>        <chr>   <chr>         <dbl>   <dbl>  <dbl>     <dbl>
#>  1 Altai_Nean… Chimp.REF    Deniso… Mbuti.DG     0.0196 6.07e-4   32.4 1.32e-229
#>  2 Altai_Nean… Denisova.DG  Chimp.… Mbuti.DG    -0.0129 3.64e-4  -35.6 2.22e-277
#>  3 Altai_Nean… Mbuti.DG     Chimp.… Denisova.DG -0.0326 5.22e-4  -62.5 0.       
#>  4 Altai_Nean… Chimp.REF    Deniso… Russia_Ust…  0.0180 6.87e-4   26.3 6.43e-152
#>  5 Altai_Nean… Denisova.DG  Chimp.… Russia_Ust… -0.0152 4.46e-4  -34.0 4.67e-254
#>  6 Altai_Nean… Russia_Ust_… Chimp.… Denisova.DG -0.0332 5.55e-4  -60.0 0.       
#>  7 Altai_Nean… Chimp.REF    Deniso… Switzerlan…  0.0181 6.63e-4   27.3 1.09e-164
#>  8 Altai_Nean… Denisova.DG  Chimp.… Switzerlan… -0.0150 4.64e-4  -32.3 6.06e-229
#>  9 Altai_Nean… Switzerland… Chimp.… Denisova.DG -0.0331 5.74e-4  -57.7 0.       
#> 10 Altai_Nean… Chimp.REF    Deniso… Vindija.DG  -0.0771 6.98e-4 -110.  0.       
#> # … with 95 more rows

Interactive browser app

ADMIXTOOLS 2 also has a simple point-and-click interface. This makes it easy to explore many qpAdm or qpGraph models at the same time, for example by allowing you to build and change admixture graphs interactively. Typing the following command in the R console launches the app:

run_shiny_admixtools()

app demo

Documentation

One of the design goals behind ADMIXTOOLS 2 is to make the algorithms more transparent, so that the steps leading from from genotype data to conclusions about demographic history are easier to follow.

To this end, all ADMIXTOOLS 2 functions are documented. You can also take a look at the tutorial, read more about how ADMIXTOOLS 2 computes f-statistics and standard errors, and what you can do with admixture graphs.

For even greater transparency, many of the core functions are implemented twice: In C++ for performance (used by default), and in R, which makes it easier to trace the computations step by step. For example, if you want to know how weights are computed in qpadm(), you can type qpadm in R to get the function code and you will see another function which is called qpadm_weights(). By default, this function will be replaced by its faster C++ version cpp_qpadm_weights(). But you can still see what it’s doing without reading the C++ code by typing admixtools:::qpadm_weights. And you can tell qpadm() to use the R versions instead of the C++ versions by calling qpadm(cpp = FALSE).

Contact

For questions, feature requests, and bug reports, please contact Robert Maier under rmaier@broadinstitute.org.

Cite ADMIXTOOLS 2

If you wish to cite ADMIXTOOLS 2, you can link to this website and mention that a manuscript describing ADMIXTOOLS 2 is currently under preparation.

See also



uqrmaie1/admixtools documentation built on Sept. 22, 2020, 3:35 p.m.