Man pages for dcgerard/updog
Using Parental Data for Offspring Genotyping

bb_postPosterior inference in beta-binomial model.
bbpost_doublePosterior inference under the beta-binomial model with...
bbpost_totPosterior inference for each individual.
bb_simple_postSimple posterior inference for beta-binomial when ncounts and...
bin_postCalculates posterior probabilities of a genotype given just...
colSums_cppStupid implementation of colSums because I guess not...
dbetabinomBeta-binomial density function.
dbetabinom_cppAn Rcpp version of the 'dbetabinom'.
dbetabinom_mu_rhobeta-binomial density function in terms of mean and...
dbetabinom_mu_rho_cppAn Rcpp version of 'dbetabinom_mu_rho'.
dbetabinom_mu_rho_cpp_doubledouble version of betabinomial density.
dbeta_ddDerivative of betabinomial density w.r.t. original bias...
dbeta_depsDerivative of beta density w.r.t. sequencing error rate.
dbeta_dhDerivative of overdispersion parameter of beta density.
dbeta_dlDerivative of beta density w.r.t. unconstrained...
dbeta_dpropDerivative of mean of beta density.
dbeta_drDerivative of beta(x|n, xi, r), where r = log(h) from...
dbeta_dr_ellSame as 'dbeta_dh', but with same inputs as 'dbeta_ds' and...
dbeta_dsDerivative of betabinomial density w.r.t. bias parameter.
dbeta_dtauDerivative of beta(x|n, xi, tau).
dbeta_dtau_withxiDerivative of overdispersion parameter with mean already...
dd_dsJust a wrapper for 'std::exp'.
deps_dellDerivative of exp(ell) / (1 + exp(ell))
df_depsReturns derivative of p(1 - eps) + (1 - p) * eps
dh_drJust a wrapper for 'std::exp'.
dh_dtauDerivative of h(tau) = (1 - tau) / tau.
dhyper_cppVectorized version of 'dhyper' for C++ implementation.
dupdogReturns log-likelihood of 'updog' object.
dxi_ddDerivative w.r.t. d of xi(d, f) = f / (d * (1 - f) + f)
dxi_dfReturns derivative to f / (d * (1 - f) + f)
est_seq_errorEstimate sequencing error from counts.
est_seq_postUse posterior probabilities to update the estimated...
expitThe expit function.
fn_cov_mleWrapper for 'obj_offspring_reparam'.
get_cov_mleCalculate the negative inverse hessian of the parameters from...
get_dimnameReturns a vector character strings that are all of the...
get_out_propE step in EM algorithm for a single individual.
get_parent_outpropE-step for the parents.
get_prob_genoRcpp function to get genotype probabilities assuming either...
get_pvecGets all possible binomial probabilities for a given ploidy,...
get_q_arrayDerive the probabilities of an offspring's genotype given its...
get_q_array_cppRcpp implementation of 'get_q_array'.
get_transition_matGet the transition probabilities from going from one ploidy...
good_bb_objObjective function for non-outlier model
grad_offspringGradient of 'obj_offspring_reparam'.
grad_offspring_matGradient of 'obj_offspring_reparam' for each individual.
grad_offspring_mat_originalGradient of 'obj_offspring' for each individual. This is in...
grad_offspring_originalGradient of 'obj_offspring' using the original...
grad_offspring_weightsGradient of 'obj_offspring_weights_reparam'
grad_offspring_weights_originalGradient of 'obj_offspring_weights' using original...
grad_parentGradient of 'obj_parent' (when 'outlier = FALSE') with...
grad_parent_reparamThe gradient of 'obj_parent_reparam' with respect to 's',...
grad_wrapp_allwrapper for 'grad_offspring_weights'
is.updogTests if its argument is an updog.
logsumexpLog-sum-exponential trick that I use all the time.
obj_offspringObjective function for the offspring.
obj_offspring_reparamJust a reparameterization of 'obj_offspring'.
obj_offspring_vecVector of objective functions for offspring.
obj_offspring_weightsSame thing as 'obj_offspring', but each sample's log-density...
obj_offspring_weights_reparamReparameterization of 'obj_offspring_weights'.
obj_parentParent contribution to objective function.
obj_parent_reparamA reparameterization of 'obj_parent'
obj_wrapp_allwrapper for 'obj_offspring_weights_reparam'
out_grad_parentGradient function for 'dbetabinom_mu_rho_cpp_double'.
out_grad_wrappWrapper for 'outlier_grad'.
outlier_bb_objObjective function for outlier model.
outlier_gradThe gradient of 'outlier_obj'.
outlier_objObjective function of outlier part in EM step
out_obj_wrappWrapper for 'outlier_obj'.
pbiasReturns the probability of seeing the reference allele after...
pbias_doubleA double version of 'pbias'.
plot_beta_distPlot the beta distribution.
plot_beta_dist_ggPlot the beta distribution using ggplot2.
plot_genoMake a genotype plot.
plot_geno_baseThe base R graphics version of 'plot_geno'.
plot_problinesPlots the genotype lines for a given sequencing error rate,...
plot.updogDraw a genotype plot from the output of 'updog'.
rbetabinom_mu_rhoDraw from beta-binomial distribution parameterized by mean...
rupdogSamples counts using the parameter values in an 'updog'...
screen_oracleReturns the distribution of proportion of individuals...
snpdatGBS data from Shirasawa et al (2017)
summary.updogSummary method for class "'updog'".
up_bb_fixEM iteration for overdispersed binomial mixture model.
up_bb_objObjective function for overdispersed binomial mixture model
update_goodUpdate the OK points
updogUsing Parental Data for Offspring Genotyping.
updog_iterateIterate between indiividual level estimates and joint...
updog_maximizeEstimate parental genotypes using offspring genotypes.
updog_mcmcThe updog Gibbs sampler to jointly estimate the parental and...
updog_oldUsing Parental Data for Offspring Genotyping.
updog_update_allThis is the main optimization function for updog.
updog_vanillaUsing Parental Data for Offspring Genotyping.
up_fixFixed-point iteration for updog EM.
up_max_bbEM algorithm for over-dispersed mixture model.
up_objThe objective function
dcgerard/updog documentation built on April 12, 2018, 9:23 p.m.