polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

ExpectedHindHe

R Documentation

Simulate Data to Get Expected Distribution of Hind/He

Description

These functions were created to help users determine an appropriate cutoff for filtering loci based on H_{ind}/H_E after running HindHe and InbreedingFromHindHe. ExpectedHindHe takes allele frequencies, sample size, and read depths from a RADdata object, simulates genotypes and allelic read depths from these assuming Mendelian inheritance, and then estimates H_{ind}/H_E for each simulated locus. ExpectedHindHeMapping performs similar simulation and estimation, but in mapping populations based on parental genotypes and expected distribution of progeny genotypes. SimGenotypes, SimGenotypesMapping, and SimAlleleDepth are internal functions used by ExpectedHindHe and ExpectedHindHeMapping but are provided at the user level since they may be more broadly useful.

Usage

ExpectedHindHe(object, ploidy = object$possiblePloidies[[1]], inbreeding = 0,
               overdispersion = 20, contamRate = 0, errorRate = 0.001,
               reps = ceiling(5000/nLoci(object)),
               quiet = FALSE, plot = TRUE)

ExpectedHindHeMapping(object, ploidy = object$possiblePloidies[[1]],
                      n.gen.backcrossing = 0, n.gen.selfing = 0,
                      overdispersion = 20, contamRate = 0, errorRate = 0.001,
                      freqAllowedDeviation = 0.05, 
                      minLikelihoodRatio = 10, reps = ceiling(5000/nLoci(object)),
                      quiet = FALSE, plot = TRUE)

SimGenotypes(alleleFreq, alleles2loc, nsam, inbreeding, ploidy)

SimGenotypesMapping(donorGen, recurGen, alleles2loc, nsam,
                    ploidy.don, ploidy.rec,
                    n.gen.backcrossing, n.gen.selfing)

SimAlleleDepth(locDepth, genotypes, alleles2loc, overdispersion = 20,
               contamRate = 0, errorRate = 0.001)

Arguments

`object`	A `RADdata` object.
`ploidy`	A single integer indicating the ploidy to use for genotype simulation. For `ExpectedHindHe` and `ExpectedHindHeMapping`, this number will be multiplied by the values in `GetTaxaPloidy(object)` then divided by two to determine the ploidy of each individual for simulation.
`inbreeding`	A number ranging from 0 to 1 indicating the amount of inbreeding (`F`). This represents inbreeding from all sources (population structure, self-fertilization, etc.) and can be estimated with `InbreedingFromHindHe`.
`overdispersion`	Overdispersion parameter as described in `AddGenotypeLikelihood`. Lower values will cause allelic read depth distributions to deviate further from expectations based on allele copy number.
`contamRate`	Sample cross-contamination rate to simulate. Although 0 is the default, 0.001 is also reasonable.
`errorRate`	Sequencing error rate to simulate. For Illumina reads, 0.001 is a reasonable value. An error is assumed to have an equal chance of converting an allele to any other allele at the locus, although this is somewhat of an oversimplification.
`reps`	The number of times to simulate the data and estimate `H_{ind}/H_E`. This can generally be left at the default, but set it higher than 1 if you want to see within-locus variance in the estimate.
`quiet`	Boolean indicating whether to suppress messages and results printed to console.
`plot`	Boolean indicating whether to plot a histogram of `H_{ind}/H_E` values.
`n.gen.backcrossing`	An integer indicating the number of generations of backcrossing.
`n.gen.selfing`	An integer indicating the number of generations of self-fertilization.
`freqAllowedDeviation`	The amount by which allele frequencies are allowed to deviate from expected allele frequencies. See `AddAlleleFreqMapping`.
`minLikelihoodRatio`	Minimum likelihood ratio for determining the most likely parental genotypes. See `GetLikelyGen`.
`alleleFreq`	A vector of allele frequencies, as can be found in the `$alleleFreq` slot of a `RADdata` object after running `AddAlleleFreqHWE`.
`alleles2loc`	An integer vector assigning alleles to loci, as can be found in the `$alleles2loc` slot of a `RADdata` object.
`nsam`	An integer indicating the number of samples (number of taxa) to simulate.
`donorGen`	A vector indicating genotypes of the donor parent (which can be either parent if backcrossing was not performed), with one value for each allele in the dataset, and numbers indicating the copy number of each allele.
`recurGen`	A vector indicating genotypes of the recurrent parent, as with `donorGen`.
`ploidy.don`	A single integer indicating the ploidy of the donor parent.
`ploidy.rec`	A single integer indicating the ploidy of the recurrent parent.
`locDepth`	An integer matrix indicating read depth at each taxon and locus. Formatted as the `$locDepth` slot of a `RADdata` object, notably with columns named by locus number rather than locus name.
`genotypes`	A numeric matrix, formatted as the output of `GetProbableGenotypes` or `SimGenotypes`, indicating genotypes as allele copy number.

Details

To prevent highly inflated values in the output, ExpectedHindHe filters loci with minor allele frequencies below five times the sequencing error rate.

Value

ExpectedHindHe and ExpectedHindHeMapping invisibly return a matrix, with loci in rows and reps in columns, containing H_{ind}/H_E from the simulated loci.

SimGenotypes and SimGenotypesMapping return a numeric matrix of allele copy number, with samples in rows and alleles in columns, similar to that produced by GetProbableGenotypes.

SimAlleleDepth returns an integer matrix of allelic read depth, with samples in rows and alleles in columns, similar to the $alleleDepth slot of a RADdata object.

Author(s)

Lindsay V. Clark

References

Clark, L. V., Mays, W., Lipka, A. E. and Sacks, E. J. (2022) A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes. BMC Bioinformatics 23, 101, doi:10.1186/s12859-022-04635-9.

Examples

# Load dataset for the example
data(exampleRAD)
exampleRAD <- AddAlleleFreqHWE(exampleRAD)

# Simulate genotypes
simgeno <- SimGenotypes(exampleRAD$alleleFreq, exampleRAD$alleles2loc, 10, 0.2, 2)

# Simulate reads
simreads <- SimAlleleDepth(exampleRAD$locDepth[1:10,], simgeno, exampleRAD$alleles2loc)

# Get expected Hind/He distribution if all loci in exampleRAD were well-behaved
ExpectedHindHe(exampleRAD, reps = 10)

# Mapping population example
data(exampleRAD_mapping)
exampleRAD_mapping <- SetDonorParent(exampleRAD_mapping, "parent1")
exampleRAD_mapping <- SetRecurrentParent(exampleRAD_mapping, "parent2")
exampleRAD_mapping <- AddAlleleFreqMapping(exampleRAD_mapping,
                                           expectedFreqs = c(0.25, 0.75),
                                           allowedDeviation = 0.08)
exampleRAD_mapping <- AddGenotypeLikelihood(exampleRAD_mapping)
exampleRAD_mapping <- EstimateParentalGenotypes(exampleRAD_mapping,
                                                n.gen.backcrossing = 1)

simgenomap <- SimGenotypesMapping(exampleRAD_mapping$likelyGeno_donor[1,],
                                  exampleRAD_mapping$likelyGeno_recurrent[1,],
                                  exampleRAD_mapping$alleles2loc,
                                  nsam = 10, ploidy.don = 2, ploidy.rec = 2,
                                  n.gen.backcrossing = 1,
                                  n.gen.selfing = 0)
                                  
ExpectedHindHeMapping(exampleRAD_mapping, n.gen.backcrossing = 1, reps = 10)

lvclark/polyRAD documentation built on Jan. 15, 2024, 4:19 a.m.