gl.run.EMIBD9: Run program EMIBD9

In dartR.captive: Analysing 'SNP' Data to Support Captive Breeding

Run program EMIBD9

Description

Run program EMIBD9

Usage

gl.run.EMIBD9(
  x,
  outfile = "EMIBD9_Res.ibd9",
  outpath = tempdir(),
  emibd9.path = getwd(),
  Inbreed = FALSE,
  palette_convergent = NULL,
  parallel = FALSE,
  ncores = 1,
  ISeed = 42,
  plot.out = TRUE,
  plot.dir = NULL,
  plot.file = NULL,
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP data [required].
outfile	A string, giving the path and name of the output file [default "EMIBD9_Res.ibd9"].
outpath	Path where to save the output file. Use outpath=getwd() or outpath='.' when calling this function to direct output files to your working or current directory [default tempdir(), mandated by CRAN].
emibd9.path	Path to the folder emidb files. Please note there are 2 different executables depending on your OS: EM_IBD_P.exe (=Windows) EM_IBD_P (=Mac, Linux). You only need to point to the folder (the function will recognise which OS you are running) [default getwd()].
Inbreed	A Boolean, taking values TRUE or FALSE to indicate inbreeding is not and is allowed in estimating IBD coefficients [default FALSE].
palette_convergent	A continuous palette function for the relatedness values [default NULL].
parallel	Use parallelisation[default FALSE].
ncores	How many cores should be used [default 1].
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]

Details

The results of EMIBD9 include the identical in state (IIS) values for each mode (S1 - 9) and nine condensed identical by descent (IBD) modes (\delta1 - \delta9) as well as the relatedness coefficient (r). Alleles are IIS if they are the same. Similarly, IBD describes a matching allele between two individuals that has been inherited from a common ancestor or common gene. In a pairwise comparison, \delta 1 to \delta 9 are the probabilities associated with each IBD mode. In inbreeding populations, only \delta 1 to \delta 6 can can occur. In contrast, \delta 7 to \delta 9 can only occur in large, panmictic outbred populations.

EMIBD9 uses an expectation maximization (EM) algorithm based on the maximum likelihood expectations (MLE) of \delta to estimate both allele frequencies (p) and \delta jointly from genotype data. By iteratively calculating p and \delta, relatedness can be modified to reduce biases due to small sample sizes. Wang J. (2022) suggest the resulting r coefficient is therefore more robust compared to previous methods.

The kinship coefficient is the probability that two alleles at a random locus drawn from two individuals are IBD.

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)|

|Half-cousin | 0.031 | (0.012, 0.055)|

|Second cousin | 0.016 | (0.004, 0.031)|

|Half-second cousin | 0.008 | (0.001, 0.020)|

|Third cousin | 0.004 | (0.000, 0.012)|

|Unrelated | 0 | - |

For greater detail on the methods employed by EMIBD9, we encourage you to read Wang, J. (2022).

Download the program from here:

https://www.zsl.org/about-zsl/resources/software/emibd9

For Windows, Mac and Linux install the program then point to the folder where you find: EM_IBD_P.exe (=Windows) and EM_IBD_P (=Mac, Linux). If running really slow you may want to create the files using the function and then run in parallel using the documentation provided by the authors [you need to have mpiexec installed].

Value

A matrix with pairwise relatedness

Author(s)

Custodian: Luis Mijangos – 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.

Examples

## Not run: 
#To run this function needs EMIBD9 installed in your computer
t1 <- gl.filter.allna(platypus.gl)
res_rel <- gl.run.EMIBD9(t1)

## End(Not run)

dartR.captive documentation built on April 3, 2025, 7:34 p.m.