admixr (version 0.9.1)

qpAdm: 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.

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
)
# }
# NOT RUN {
# }