R/qpAdm.R
qpAdm_rotation.Rd
Fit qpAdm models based on the rotation strategy described in Harney et al. 2020 (bioRxiv)
qpAdm_rotation(
data,
target,
candidates,
minimize = TRUE,
nsources = 2,
ncores = 1,
fulloutput = FALSE,
params = NULL
)
EIGENSTRAT dataset
Target population that is modeled as admixed
Potential candidates for sources and outgroups
Test also all possible subsets of outgroups? (default TRUE)
Number of sources to pull from the candidates
Number of CPU cores to utilize for model fitting
Report also 'ranks' and 'subsets' analysis from qpAdm in addition to the admixture proportions results? (default FALSE)
Named list of parameters and their values to be passed to
qpAdm()
.
qpAdm list with proportions, ranks and subsets elements (as with a traditional qpAdm run) or just the proportions (determined by the value of the 'fulloutput' argument)
if (FALSE) # download an example genomic data set and prepare it for analysis
snps <- eigenstrat(download_data(dirname = tempdir()))
# find the set of most likely two-source qpAdm models of
# a French individual - produce only the 'proportions'
# qpAdm summary
models <- qpAdm_rotation(
data = snps,
target = "French",
candidates = c("Dinka", "Mbuti", "Yoruba", "Vindija",
"Altai", "Denisova", "Chimp"),
minimize = TRUE,
nsources = 2,
ncores = 2,
fulloutput = FALSE
)
#> Error in eval(expr, envir, enclos): object 'snps' not found