qpadm_rotate: Compute p-values for many qpadm models

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Compute p-values for many qpadm models

Description

This functions evaluates many qpadm models simultaneously by keeping the target population and the rightfix populations fixed, and distributing the leftright populations by keeping some in the set of left population and adding the remaining populations to the right populations. (See details for an example of how models are generated)

Usage

qpadm_rotate(
  f2_blocks,
  leftright,
  target,
  rightfix = NULL,
  full_results = FALSE,
  verbose = TRUE
)

Arguments

f2_blocks	3d array of blocked f2 statistics, output of f2_from_precomp.
leftright	Populations which will be distributed between left and right
target	Target population
rightfix	Populations which will be on the right side in all models
full_results	Return all output items which are returned by qpadm. By default (full_results = FALSE), weights and several other statistics will not be computed for each model, making it faster and the output more readable. If full_results = TRUE, the output will be a nested data frame where each row is one qpadm model, and each column has one data frame item from the regular qpadm output (weights, f4, rankdrop, popdrop).
verbose	Print progress updates

Details

If leftright consists of the populations L1, L2, L3, L4; rightfix is the population R; and target is T, the following models will be genrated:

(left), (right), (target)
(L1), (L2, L3, L4, R), (T)
(L2), (L1, L3, L4, R), (T)
(L3), (L1, L2, L4, R), (T)
(L4), (L1, L2, L3, R), (T)
(L1, L2), (L3, L4, R), (T)
(L1, L3), (L2, L4, R), (T)
(L1, L4), (L2, L3, R), (T)
(L2, L3), (L1, L4, R), (T)
(L2, L4), (L1, L3, R), (T)
(L3, L4), (L1, L2, R), (T)

Value

A data frame with Chi-squared statistics and p-values for each population combination

Examples

## Not run: 
pops = dimnames(example_f2_blocks)[[1]]
qpadm_rotate(example_f2_blocks, leftright = pops[1:4],
             target = pops[5], rightfix = pops[6:7])

## End(Not run)

uqrmaie1/admixtools documentation built on March 20, 2024, 8:24 a.m.