jackHWE: Hardy-Weinberg Equlibrium Jackknife
In strataG: Summaries and Population Structure Analyses of Genetic Data

Description Usage Arguments Details Value Author(s) References See Also

Test influence of samples on Hardy-Weinberg equilibrium via jackknife.

jackHWE(g, exclude.num = 1, min.hwe.samples = 5, show.progress = TRUE, ...)

jackInfluential(jack.result, alpha = 0.05)

## S3 method for class 'jack.influential'
plot(x, main = NULL, ...)

.alleleFreqFormat(x, g)

`g`	a gtypes object.
`exclude.num`	Number of samples to exclude at a time.
`min.hwe.samples`	minimum samples needed to calculate HWE.
`show.progress`	logical. Show progress of jackknife?
`...`	other arguments to be passed to `hweTest`.
`jack.result`	result from run of `jackHWE`.
`alpha`	critical value to determine if exclusion is "influential".
`x`	a matrix or data.frame where first column is sample id and second colum is locus name.
`main`	main title for influential sample plots from `plot.jack.influential`.

jackHWE: performs a HWE jackknife where all combinations of exclude.num samples are left out and HWE is recalculated
jackInfluential: calculates odds.ratios between jackknife HWE and observed HWE and identifies "influential" samples. Samples are "influential" if the observed HWE p-value is < alpha, but is > alpha when the samples are not present
plot.jack.influential: creates a cumulative frequency plot of all odds-ratios from jack.influential. A vertical dashed line marks the smallest influential exclusion

jackHWE returns a list with:

`obs`	a named vector of HWE p-values for each locus.
`jack`	a `data.frame` of HWE p-values where each row is an exclusion and columns are loci.
`gtypes`	the original `gtypes` object.

jackInfluential returns a list with:

`influential`	a `data.frame` of influential exclusions.
`allele.freqs`	a `data.frame` listing the allele frequencies of influential exclusions.
`odds.ratio`	a `matrix` of odds ratios between exclusions (rows) and loci (columns).

Eric Archer eric.archer@noaa.gov

Morin, P.A., R.G. LeDuc, F.I. Archer, K.K. Martien, R. Huebinger, J.W. Bickham, and B.L. Taylor. 2009. Significant deviations from Hardy-Weinberg equilibirum caused by low levels of microsatellite genotyping errors. Molecular Ecology Resources 9:498-504.

hweTest

strataG documentation built on Feb. 28, 2020, 9:07 a.m.