qpAdm_rotation: Fit qpAdm models based on the rotation strategy described in...

In admixr: An Interface for Running 'ADMIXTOOLS' Analyses

Description

Fit qpAdm models based on the rotation strategy described in Harney et al. 2020 (bioRxiv)

Usage

qpAdm_rotation(
  data,
  target,
  candidates,
  minimize = TRUE,
  nsources = 2,
  ncores = 1,
  fulloutput = FALSE
)

Arguments

data	EIGENSTRAT dataset
target	Target population that is modeled as admixed
candidates	Potential candidates for sources and outgroups
minimize	Test also all possible subsets of outgroups? (default TRUE)
nsources	Number of sources to pull from the candidates
ncores	Number of CPU cores to utilize for model fitting
fulloutput	Report also 'ranks' and 'subsets' analysis from qpAdm in addition to the admixture proportions results? (default FALSE)

Value

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)

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
)

## End(Not run)

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