Filter qpAdm rotation results for only 'sensible' models

Source: R/qpAdm.R

Filter for p-value larger than a specified cuttof and admixture proportions between 0 and 1.

qpAdm_filter(x, p = 0.05)

Arguments

x

Output of a qpAdm_rotation() function

p

p-value cutoff (default 0: will only filter for sensible admixture proportions)

Value

qpAdm_rotation object filtered down based on p-value

Examples

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 check_type(data, "EIGENSTRAT"): object 'snps' not found

# filter out models which can clearly be rejected
fits <- qpAdm_filter(models, p = 0.05)
#> Error in check_type(x, "admixr_result"): object 'models' not found