Calculate ancestry proportions in a set of target populations.
qpAdm(
data,
target,
sources,
outgroups,
outdir = NULL,
params = list(allsnps = "YES", summary = "YES", details = "YES")
)
EIGENSTRAT data object.
Vector of target populations (evaluated one at a time).
Source populations related to true ancestors.
Outgroup populations.
Where to put all generated files (temporary directory by default).
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).
List of three components: 1. estimated ancestry proportions 2. ranks statistics 3. analysis of patterns (all possible subsets of ancestry sources).
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 eval(expr, envir, enclos): object 'snps' not found