qpAdm_filter: Filter qpAdm rotation results for only 'sensible' models

In admixr: An Interface for Running 'ADMIXTOOLS' Analyses

Description

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

Usage

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

## 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)

admixr documentation built on July 8, 2020, 6:19 p.m.