qpAdm: Calculate ancestry proportions in a set of target...

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

Calculate ancestry proportions in a set of target populations.

Description

Calculate ancestry proportions in a set of target populations.

Usage

qpAdm(
  data,
  target,
  sources,
  outgroups,
  outdir = NULL,
  params = list(allsnps = "YES", summary = "YES", details = "YES")
)

Arguments

data	EIGENSTRAT data object.
target	Vector of target populations (evaluated one at a time).
sources	Source populations related to true ancestors.
outgroups	Outgroup populations.
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).

Value

List of three components: 1. estimated ancestry proportions 2. ranks statistics 3. analysis of patterns (all possible subsets of ancestry sources).

Examples

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

# estimate the proportion of Neandertal ancestry in a French
# individual and other associated qpAdm statistics (see detailed
# description in the tutorial vignette)
result <- qpAdm(
    target = "French",
    sources = c("Vindija", "Yoruba"),
    outgroups = c("Chimp", "Denisova", "Altai"),
    data = snps
)

## End(Not run)

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