gl.nhybrids: Creates an input file for the program NewHybrids and runs it...

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Creates an input file for the program NewHybrids and runs it if NewHybrids is installed

Description

This function compares two sets of parental populations to identify loci that exhibit a fixed difference, returns an genlight object with the reduced data, and creates an input file for the program NewHybrids using the top 200 (or hard specified loc.limit) loci. In the absence of two identified parental populations, the script will select a random set 200 loci only (method='random') or the first 200 loci ranked on information content (method='AvgPIC').

A fixed difference occurs when a SNP allele is present in all individuals of one population and absent in the other. There is provision for setting a level of tolerance, e.g. threshold = 0.05 which considers alleles present at greater than 95 a fixed difference. Only the 200 loci are retained, because of limitations of NewHybids.

If you specify a directory for the NewHybrids executable file, then the script will create the input file from the SNP data then run NewHybrids. If the directory is set to NULL, the execution will stop once the input file (default='nhyb.txt') has been written to disk. Note: the executable option will not work on a Mac; Mac users should generate the NewHybrids input file and run this on their local installation of NewHybrids.

Refer to the New Hybrids manual for further information on the parameters to set – http://ib.berkeley.edu/labs/slatkin/eriq/software/new_hybs_doc1_1Beta3.pdf

It is important to stringently filter the data on RepAvg and CallRate if using the random option. One might elect to repeat the analysis (method='random') and combine the resultant posterior probabilities should 200 loci be considered insufficient.

The F1 individuals should be homozygous at all loci for which the parental populations are fixed and different, assuming parental populations have been specified. Sampling errors can result in this not being the case, especially where the sample sizes for the parental populations are small. Alternatively, the threshold for posterior probabilities used to determine assignment (pprob) or the definition of a fixed difference (threshold) may be too lax. To assess the error rate in the determination of assignment of F1 individuals, a plot of the frequency of homozygous reference, heterozygotes and homozygous alternate (SNP) can be produced by setting plot=TRUE (the default).

Usage

gl.nhybrids(
  gl,
  outpath = tempdir(),
  p0 = NULL,
  p1 = NULL,
  threshold = 0,
  method = "random",
  plot = TRUE,
  plot_theme = theme_dartR(),
  plot_colors = two_colors,
  pprob = 0.95,
  nhyb.directory = NULL,
  BurnIn = 10000,
  sweeps = 10000,
  GtypFile = "TwoGensGtypFreq.txt",
  AFPriorFile = NULL,
  PiPrior = "Jeffreys",
  ThetaPrior = "Jeffreys",
  verbose = NULL
)

Arguments

gl	Name of the genlight object containing the SNP data [required].
outpath	Path where to save the output file [default tempdir()].
p0	List of populations to be regarded as parental population 0 [default NULL].
p1	List of populations to be regarded as parental population 1 [default NULL].
threshold	Sets the level at which a gene frequency difference is considered to be fixed [default 0].
method	Specifies the method (random or AvgPIC) to select 200 loci for NewHybrids [default random].
plot	If TRUE, a plot of the frequency of homozygous reference, heterozygotes and homozygous alternate (SNP) is produced for the F1 individuals [default TRUE, applies only if both parental populations are specified].
plot_theme	User specified theme [default theme_dartR()].
plot_colors	Vector with two color names for the borders and fill [default two_colors].
pprob	Threshold level for assignment to likelihood bins [default 0.95, used only if plot=TRUE].
nhyb.directory	Directory that holds the NewHybrids executable file e.g. C:/NewHybsPC [default NULL].
BurnIn	Number of sweeps to use in the burn in [default 10000].
sweeps	Number of sweeps to use in computing the actual Monte Carlo averages [default 10000].
GtypFile	Name of a file containing the genotype frequency classes [default TwoGensGtypFreq.txt].
AFPriorFile	Name of the file containing prior allele frequency information [default NULL].
PiPrior	Jeffreys-like priors or Uniform priors for the parameter pi [default Jeffreys].
ThetaPrior	Jeffreys-like priors or Uniform priors for the parameter theta [default Jeffreys].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Value

The reduced genlight object, if parentals are provided; output of NewHybrids is saved to the working directory.

Author(s)

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

References

Anderson, E.C. and Thompson, E.A.(2002). A model-based method for identifying species hybrids using multilocus genetic data. Genetics. 160:1217-1229.

Examples

## Not run: 
m <- gl.nhybrids(testset.gl, 
p0=NULL, p1=NULL,
nhyb.directory='D:/workspace/R/NewHybsPC', # Specify as necessary
outpath="D:/workspace",  # Specify as necessary, usually getwd() [= workspace]
BurnIn=100,
sweeps=100,
verbose=3)

## End(Not run)

green-striped-gecko/dartR documentation built on Jan. 31, 2024, 10:14 a.m.