popStructTest: Population Structure Tests
In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

popStructTest

R Documentation

Population Structure Tests

Description

Conduct multiple tests of population structure / differentiation. Overall tests can be conducted for the current stratification scheme (overallTest()), or can be conducted for all unique pairs of strata (pairwiseTest()). All statistics appropriate to the ploidy of the data are estimated at once. See Note for a description of each statistic.

Usage

overallTest(
  g,
  nrep = 1000,
  by.locus = FALSE,
  hap.locus = 1,
  quietly = FALSE,
  max.cores = 1,
  ...
)

pairwiseTest(
  g,
  nrep = 1000,
  by.locus = FALSE,
  hap.locus = 1,
  quietly = FALSE,
  max.cores = 1,
  ...
)

pairwiseMatrix(pws, stat, locus = "All")

pairwiseSummary(pws, locus = "All")

Arguments

`g`	a `gtypes` object.
`nrep`	number specifying number of permutation replicates to use for permutation test.
`by.locus`	return by-locus values of statistics? If `TRUE` the overall value will be contained in the first row, labelled `"All"`. Only applies if the ploidy of `g` is > 1 (non-haploid).
`hap.locus`	which locus to use if `g` is haploid. Can be specified by number or name.
`quietly`	logical. print progress to screen?
`max.cores`	the maximum number of cores to use to distribute replicates for permutation tests over. If set to `NULL`, the value will be what is reported by `detectCores - 1`. If `detectCores` reports `NA`, `max.cores` will be set to 1 and parallel processing will not be done.
`...`	parameters passed to `dist.dna` for computation of pairwise distance matrix for AMOVA PHIst statistic.
`pws`	a list returned from a call to `pairwiseTest()`.
`stat`	the name of a statistic in the `$result` element for pairwise comparisons returned by `pairwiseTest()`.
`locus`	the name of a single locus. If `"All"`, the overall result from all loci is returned. See `by.locus`.

Value

overallTest()

a list containing:

strata.freq: a table of the sample sizes for each stratum
result: an array with the statistic estimate and p-value for each statistic. If by.locus = FALSE or g is a haploid dataset, this is a two-dimensional array, with one row per statistic, statistic estimate in the first column and permutation test p-value in the second column. If by.locus = TRUE and g has ploidy > 1, then this is a three-dimensional array where the first dimension is loci, second dimension is statistics, and third dimension is statistic estimate and p-value.

pairwiseTest()

a list containing a list of results as described above for overallTest() for each pairwise comparison.

pairwiseMatrix()

a matrix summarizing a chosen statistic (stat) for a chosen locus (locus) between pairs of strata with the statistic estimate in the lower left and the p-value in the upper right.

pairwiseSummary()

a data frame summarizing all pairwise statistics and p-values along with strata sample sizes.

Note

The computed statistics are:

`CHIsq`	chi-squared estimate measuring random allele frequency distribution distributed across strata (haploid and diploid)
`Ho, Hs, Ht`	Nei and Kumar 2002 : observed heterozygosity (`Ho`), within population diversity (`Hs`), overall diversity (`Ht`)
`Ht_prime`	description
`Dst`	description
`Dst_prime`	description
`Fst`	For haploid data, equivalent to PHIst with pairwise distances set to 1. For diploid data,
`Fst_prime`	description
`Fis`	description
`Gst_prime`	description
`Gst_dbl_prime`	description
`Dest, Dest_Chao`	population differentiation (Jost 2008)
`wcFit, wcFst, wcFit`	(Weir and Cockerham 1984)
`PHIst`	Haploid AMOVA estimate of differentiation derived from matrix of pairwise distances between sequences. See `dist.dna` for details on distance computation. (Excoffier et al 1992)

Author(s)

Eric Archer eric.archer@noaa.gov

References

Excoffier, L., Smouse, P.E. and Quattro, J.M. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491. Jost, L. 2008. GST and its relatives do not measure differentiation. Molecular Ecology 17:4015-4026. Nei M. and Chesser R. 1983. Estimation of fixation indexes and gene diversities. Annals of Human Genetics 47:253-259. Nei M. 1987. Molecular Evolutionary Genetics. Columbia University Press Weir, B.S. and Cockerham, C.C. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370. Weir, B.S. and Hill, W.G. 2002. Estimating F-statistics. Annual Review of Genetics 36:721–750.

Examples

# An overall test with microsatellite data
data(msats.g)
ovl <- overallTest(msats.g, nrep = 100)
ovl

#' A pairwise test with control region sequences
data(dloop.g)
pws <- pairwiseTest(dloop.g, nrep = 100)
pws

EricArcher/strataG documentation built on Feb. 12, 2023, 4:11 a.m.