dartR.captive (version 1.0.2)

gl.sim.relatedness: Simulate relatedness estimates.

Description

A simulation based tool to estimate different degrees of relatedness using genlight object to bootstrap the results of kinship estimates. This method uses EMIBD9 (Wang, J. 2022).

Below is a table modified from Speed & Balding (2015) showing kinship values, and their confidence intervals (CI), for different relationships that could be used to guide the choosing of the relatedness threshold in the function.

|Relationship |Kinship | 95

|Identical twins/clones/same individual | 0.5 | - |

|Sibling/Parent-Offspring | 0.25 | (0.204, 0.296)|

|Half-sibling | 0.125 | (0.092, 0.158)|

|First cousin | 0.062 | (0.038, 0.089)|

|Unrelated | 0 | - |

Usage

gl.sim.relatedness(
  x,
  rel = "full.sib",
  nboots = 10,
  emibd9.path = getwd(),
  conf = 0.95,
  iseed = 42,
  plot.out = TRUE,
  plot.dir = NULL,
  plot.file = NULL,
  verbose = NULL
)

Value

Summary statistics of chosen relatedness relationship and a histogram of relatedness values showing the mean.

Arguments

x

Name of the genlight object containing the SNP data [required].

rel

The degree of relatedness you wish to simulate. One of, 'full.sib', 'half.sib','first.cousin' [default 'full.sib'].

nboots

The number of simulation replicates you wish to perform [default 10].

emibd9.path

The location of all necessary files to run EMIBD9 (read more at gl.run.EMIBD9)

conf

The specified threshold for confidence interval calculation from simulated relatedness values [default 0.95]

iseed

An integer used to seed the random number generator [default 42].

plot.out

A boolean that indicates whether to plot the results [default TRUE].

plot.dir

Directory to save the plot RDS files [default as specified by the global working directory or tempdir()]

plot.file

Name for the RDS binary file to save (base name only, exclude extension) [default NULL]

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL, unless specified using gl.set.verbosity]

Author

Custodian: Sam Amini -- Post to https://groups.google.com/d/forum/dartr

References

• Wang, J. (2022). A joint likelihood estimator of relatedness and allele frequencies from a small sample of individuals. Methods in Ecology and Evolution, 13(11), 2443-2462.

  Speed, D., Balding, D. Relatedness in the post-genomic era: is it still useful?. Nat Rev Genet 16, 33–44 (2015).

Examples

if (FALSE) {
#To run this function needs EMIBD9 installed in your computer
}