Package index • segtest

All functions

beta_bounds(): Bounds on the distortion at simplex loci caused by double reduction.

chisq_g() chisq_g4(): Chi Square test when genotypes are known

chisq_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.

multi_lrt(): Parallelized likelihood ratio test for segregation distortion.

multidog_to_g(): Converts multidog output to a format usable for seg_multi() and multi_lrt()

n_pp_mix(): Number of mixture components

nextElem(<arrayiter>): Next element in an array

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

po_gl(): Generate genotype likelihoods from offspring genotypes.

polymapr_test(): Run segregation distortion tests as implemented in the polymapR package.

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 ufit2 ufit3: Genotype data from Cappai et al. (2020)