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

In admixr: An Interface for Running 'ADMIXTOOLS' Analyses

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 documentation built on July 8, 2020, 6:19 p.m.