qpwave: Estimate admixture waves

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Estimate admixture waves

Description

qpwave compares two sets of populations (left and right) to each other. It estimates a lower bound on the number of admixtue waves that went from left into right, by comparing a matrix of f4-statistics to low-rank approximations. For a rank of 0 this is equivalent to testing whether left and right form clades relative to each other.

Usage

qpwave(
  data,
  left,
  right,
  fudge = 1e-04,
  boot = FALSE,
  constrained = FALSE,
  cpp = TRUE,
  verbose = TRUE
)

Arguments

data	The input data in the form of: A 3d array of blocked f2 statistics, output of f2_from_precomp or extract_f2 A directory with f2 statistics The prefix of a genotype file
left	Left populations (sources)
right	Right populations (outgroups)
fudge	Value added to diagonal matrix elements before inverting
boot	If FALSE (the default), block-jackknife resampling will be used to compute standard errors. Otherwise, block-bootstrap resampling will be used to compute standard errors. If boot is an integer, that number will specify the number of bootstrap resamplings. If boot = TRUE, the number of bootstrap resamplings will be equal to the number of SNP blocks.
constrained	Constrain admixture weights to be non-negative
cpp	Use C++ functions. Setting this to FALSE will be slower but can help with debugging.
verbose	Print progress updates

Value

qpwave returns a list with up to two data frames describing the model fit:

1. f4 A data frame with estimated f4-statistics

2. rankdrop: A data frame describing model fits with different ranks, including p-values for the overall fit and for nested models (comparing two models with rank difference of one). A model with L left populations and R right populations has an f4-matrix of dimensions (L-1)*(R-1). If no two left population form a clade with respect to all right populations, this model will have rank (L-1)*(R-1).

   • f4rank: Tested rank

   • dof: Degrees of freedom of the chi-squared null distribution: (L-1-f4rank)*(R-1-f4rank)

   • chisq: Chi-sqaured statistic, obtained as ⁠E'QE⁠, where E is the difference between estimated and fitted f4-statistics, and Q is the f4-statistic covariance matrix.

   • p: p-value obtained from chisq as pchisq(chisq, df = dof, lower.tail = FALSE)

   • dofdiff: Difference in degrees of freedom between this model and the model with one less rank

   • chisqdiff: Difference in chi-squared statistics

   • p_nested: p-value testing whether the difference between two models of rank difference 1 is significant

References

Patterson, N. et al. (2012) Ancient admixture in human history. Genetics

Haak, W. et al. (2015) Massive migration from the steppe was a source for Indo-European languages in Europe. Nature (SI 10)

See Also

qpadm

Examples

left = c('Altai_Neanderthal.DG', 'Vindija.DG')
right = c('Chimp.REF', 'Mbuti.DG', 'Russia_Ust_Ishim.DG', 'Switzerland_Bichon.SG')
qpwave(example_f2_blocks, left, right)

uqrmaie1/admixtools documentation built on Nov. 3, 2024, 12:56 a.m.