admixr: qpWave – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

qpWave

Find the most likely number of ancestry waves using the qpWave method.

Description

Given a set of 'left' populations, estimate the lowest number of necessary admixture sources related to the set of 'right' populations.

Usage

qpWave(
  data,
  left,
  right,
  maxrank = NULL,
  details = FALSE,
  outdir = NULL,
  params = NULL
)

Arguments

`data`	EIGENSTRAT data object.
`left, right`	Character vectors of populations labels.
`maxrank`	Maximum rank to test for.
`details`	Return the A, B matrices used in rank calculations?
`outdir`	Where to put all generated files (temporary directory by default).
`params`	Named list of parameters and their values.

Details

It has been shown (Reich, Nature 2012 - Reconstructing Native American population history) that if the 'left' populations are mixtures of N different sources related to the set of 'right' populations, the rank of the matrix of the form f_4(left_i, left_j; right_k, right_l) will have a rank N - 1. This function uses the ADMIXTOOLS command qpWave to find the lowest possible rank of this matrix that is consistent with the data.

Value

Table of rank test results.

Examples

## Not run: # download example data set and prepare it for analysis
snps <- eigenstrat(download_data(dirname = tempdir()))

# run the qpWave wrapper (detailed description in the tutorial vignette)
result <- qpWave(
     left = c("French", "Sardinian", "Han"),
     right = c("Altai", "Yoruba", "Mbuti"),
     data = snps
)

## End(Not run)

admixr

An Interface for Running 'ADMIXTOOLS' Analyses

v0.9.1

MIT + file LICENSE

Authors

Martin Petr [aut, cre] (<https://orcid.org/0000-0003-4879-8421>)

Initial release