Filter qpAdm rotation results for only 'sensible' models
Filter for p-value larger than a specified cuttof and admixture proportions between 0 and 1.
qpAdm_filter(x, p = 0.05)
x |
Output of a qpAdm_rotation() function |
p |
p-value cutoff (default 0: will only filter for sensible admixture proportions) |
qpAdm_rotation object filtered down based on p-value
## Not run: # 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
)
# filter out models which can clearly be rejected
fits <- qpAdm_filter(models, p = 0.05)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.