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

In bodkan/admixr: An Interface for Running 'ADMIXTOOLS' Analyses

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. For instance, params = list(allsnps = "YES") or params = list(blgsize = 0.01) (or an arbitrary combination of parameters using a list with multiple named elements).

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)

bodkan/admixr documentation built on Feb. 20, 2025, 4:45 p.m.