Man pages for dcgerard/updog
Flexible Genotyping for Polyploids

ashpen_funPenalty on pivec used when 'model = "ash"' in 'flexdog'.
betabinomThe Beta-Binomial Distribution
compute_all_log_bbCalculates the log-density for every individual by snp by...
compute_all_phifkComputes Phi^{-1}(F(k|K,alpha_j,rho_i)) for all possible...
compute_all_post_probComputes every posterior probability for each dosage level...
convolveConvolution between two discrete probability mass functions...
dbernbinomSpecial case of betabinomial where the beta is bernoulli mu.
dbetabinom_alpha_beta_doubleDensity function of betabinomial with the shape...
dbetabinom_doubleThe density function of the beta-binomial distribution.
dc_dtauDerivative of c = (1 - tau) / tau with respect to tau.
df_depsDerivative of f with respect to eps.
dlbeta_dcDerivative of the log-beta density with respect to c where c...
dlbeta_depsDerivative of the log-beta-binomial density with respect to...
dlbeta_dhDerivative of log-betabinomial density with respect to bias...
dlbeta_dtauDerivative of the log-beta-binomial density with respect to...
dlbeta_dxiDerivative of the log-betabinomial density with respect to...
doutdistThe outlier distribution we use. Right now it is just a beta...
dpen_depsDerivative of -log(epsilon(1 - epsilon)) - (logit(epsilon) -...
dpen_dhDerivative of -log(h) - (log(h) - mu_h)^2 / (2sigma_h^2) with...
dr_penPenalty used in 'update_dr'.
dxi_dfDerivative of xi with respect to f.
dxi_dhDerivative of xi-function with respect to bias parameter.
elboThe evidence lower bound
eta_doubleAdjusts allele dosage 'p' by the sequencing error rate 'eps'.
eta_funAdjusts allele dosage 'p' by the sequencing error rate 'eps'.
expitThe expit (logistic) function.
f1_objObjective for mixture of known dist and uniform dist.
flexdogFlexible genotyping for polyploids from next-generation...
flexdog_fullFlexible genotyping for polyploids from next-generation...
flexdog_objLog-likelihood that 'flexdog' maximizes.
flexdog_obj_outLog-likelihood that 'flexdog' maximizes when outliers are...
flex_update_pivecUpdate the distribution of genotypes from various models.
get_bivalent_probsReturns segregation probabilities, pairing representation and...
get_bivalent_probs_drDouble reduction version of 'get_bivalent_probs'.
get_conv_inner_weightsGet the inner weights used for the em update in...
get_dimnameReturns a vector character strings that are all of the...
get_hyper_weightsReturn mixture weights needed to obtain a hypergeometric...
get_inner_weightsCompute inner weights for updating the mixing proportions...
get_probk_vecObtain the genotype distribution given the distribution of...
get_q_arrayReturn the probabilities of an offspring's genotype given its...
get_uni_repGet the representation of a discrete unimodal probability...
get_wik_matE-step in 'flexdog'.
get_wik_mat_outE-step in 'flexdog' where we now allow an outlier...
grad_for_epsGradient for 'obj_for_eps'.
grad_for_mu_sigma2Gradient for 'obj_for_mu_sigma2' with respect for 'mu' and...
grad_for_mu_sigma2_wrapperGradient for 'obj_for_mu_sigma2_wrapper' with respect for...
grad_for_weighted_lbbGradient for 'obj_for_weighted_lbb'.
grad_for_weighted_lnormGradient for 'obj_for_weighted_lnorm'.
initialize_pivecInitialize 'pivec' for 'flexdog' EM algorithm.
is.flexdogTests if an argument is a 'flexdog' object.
is.mupdogTests if its argument is a mupdog object.
logitThe logit function.
log_sum_expLog-sum-exponential trick.
log_sum_exp_2Log-sum-exponential trick using just two doubles.
mupdogMulti-SNP updog.
mupoutA mupdog fit of the 'uitdewilligen' data.
obj_for_alphaObjective function when updating alpha
obj_for_epsObjective function for updating sequencing error rate, bias,...
obj_for_mu_sigma2Objective function when updating mu and sigma2.
obj_for_mu_sigma2_wrapperWrapper for 'obj_for_mu_sigma2' so that I can use it in...
obj_for_rhoObjective function when updating a single inbreeding...
obj_for_weighted_lbbObjective function for updating the beta-binomial genotype...
obj_for_weighted_lnormObjective funtion for updating discrete normal genotype...
oracle_corCalculates the correlation between the true genotype and an...
oracle_cor_from_jointCalculate the correlation of the oracle estimator with the...
oracle_jointThe joint probability of the genotype and the genotype...
oracle_misCalculate oracle misclassification error rate.
oracle_mis_from_jointGet the oracle misclassification error rate directly from the...
oracle_mis_vecReturns the oracle misclassification rates for each genotype.
oracle_mis_vec_from_jointGet the oracle misclassification error rates (conditional on...
oracle_plotConstruct an oracle plot from the output of 'oracle_joint'.
pbetabinom_doubleThe distribution function of the betabinomial. This is...
pen_biasPenalty on bias parameter.
pen_seq_errorPenalty on sequencing error rate.
pivec_from_segmatsFunction to get the segregation probabilities from the...
plot.flexdogDraw a genotype plot from the output of 'flexdog'.
plot_genoMake a genotype plot.
plot.mupdogDraw a genotype plot from the output of 'mupdog'.
post_probVariational posterior probability of having 'dosage' A...
pp_brent_objObjective function when doing Brent's method in...
qbetabinom_doubleThe quantile function of the beta-binomial distribution...
rbetabinom_intOne draw from the beta-binomial distribution parameterized by...
rflexdogSimulate GBS data from the 'flexdog' likelihood.
rgenoSimulate individual genotypes from one of the supported...
snpdatGBS data from Shirasawa et al (2017)
summary.mupdogProvides some summaries from the output of 'mupdog'.
uitdewilligenSubset of individuals and SNPs from Uitdewilligen et al...
uni_emEM algorithm to fit weighted ash objective.
uni_em_constEM algorithm to fit weighted ash objective with a uniform...
uni_objObjective function optimized by 'uni_em'.
uni_obj_constObjective function optimized by 'uni_em_const'.
update_drSame as 'update_pp_f1' but I exclusively use the EM (instead...
update_pp_f1Function to update the parameters in the preferential pairing...
update_pp_s1Same as 'update_pp_f1' but only allow s1.
update_RUpdate the underlying correlation matrix.
updog'updog' Flexible Genotyping for Polyploids
wemGeneralized version of 'uni_em'.
xi_doubleAdjusts allele dosage 'p' by the sequencing error rate 'eps'...
xi_funAdjusts allele dosage 'p' by the sequencing error rate 'eps'...
dcgerard/updog documentation built on Aug. 19, 2018, 11:33 p.m.