Tests for Segregation Distortion in Polyploids

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Documentation for package ‘segtest’ version 2.0.0

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beta_bounds Bounds on the distortion at simplex loci caused by double reduction.
chisq_g Chi Square test when genotypes are known
chisq_g4 Chi Square test when genotypes are known
chisq_gl Chi-Sq for GL
chisq_gl4 Chi-Sq for GL
drbounds Upper bounds on double reduction rates.
em_li EM algorithm from Li (2011)
gamfreq Gamete frequencies under a generalized model
gcount_to_gvec Converts genotype counts to genotype vectors.
gf_freq Genotype frequencies of an F1 population under a generalized model.
gvec_to_gcount Inverse function of 'gcount_to_gvec()'.
is_valid_2 Tests if the two parameter model is valid
iter.array Iterator over array
like_gknown_2 Likelihood under three parameter model when genotypes are known
like_gknown_3 Likelihood under three parameter model when genotypes are known
like_glpknown_2 Likelihood under three parameter model when using offspring genotypes likelihoods but parent genotypes are known.
like_glpknown_3 Likelihood under three parameter model when using offspring genotypes likelihoods but parent genotypes are known.
llike_li Objective function for 'em_li()'
lrt_men_g4 Likelihood ratio test for segregation distortion with known genotypes
lrt_men_gl4 Likelihood ratio test using genotype likelihoods.
multidog_to_g Converts multidog output to a format usable for seg_multi() and multi_lrt()
multi_lrt Parallelized likelihood ratio test for segregation distortion.
nextElem.arrayiter Next element in an array
n_pp_mix Number of mixture components
offspring_geno Simulates genotypes given genotype frequencies.
offspring_gf_2 Calculates offspring genotype frequencies under the two-parameter model.
offspring_gf_3 Calculates offspring genotype frequencies under the three-parameter model.
otest_g Jointly tests for segregation distortion and number of incompatible genotypes
polymapr_test Run segregation distortion tests as implemented in the polymapR package.
po_gl Generate genotype likelihoods from offspring genotypes.
pvec_tet_2 Tetraploid gamete frequencies of gametes when one parent's genotype is known
pvec_tet_3 Tetraploid gamete frequencies of gametes when one parent's genotype is known
seg Disomic and polysomic segregation patterns
seg_lrt Test for segregation distortion in a polyploid F1 population.
seg_multi Parallelized likelihood ratio test for segregation distortion for arbitrary (even) ploidies.
simf1g Simulate genotype counts from F1 individuals
simf1gl Simulate genotype likelihoods of F1 individuals.
simgl Simulate genotype (log) likelihoods from genotype counts
three_to_two Convert from three parameters to two parameters
ufit Genotype data from Cappai et al. (2020)
ufit2 Genotype data from Cappai et al. (2020)
ufit3 Genotype data from Cappai et al. (2020)