Calculate ancestry proportions in a set of target populations.

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

if (FALSE) # 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
)
#> Error in check_type(data, "EIGENSTRAT"): object 'snps' not found