Flexible Genotyping for Polyploids


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Documentation for package ‘updog’ version 1.0.1

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A B C D E F G I L M O P Q R S U W X

updog-package 'updog' Flexible Genotyping for Polyploids

-- A --

ashpen_fun Penalty on pivec used when 'model = "ash"' in 'flexdog'.

-- B --

betabinom The Beta-Binomial Distribution

-- C --

compute_all_log_bb Calculates the log-density for every individual by snp by dosage level.
compute_all_phifk Computes Phi^{-1}(F(k|K,alpha_j,rho_i)) for all possible (i,j,k).
compute_all_post_prob Computes every posterior probability for each dosage level for each individual at each SNP.
convolve Convolution between two discrete probability mass functions with support on 0:K.

-- D --

dbernbinom Special case of betabinomial where the beta is bernoulli mu.
dbetabinom The Beta-Binomial Distribution
dbetabinom_alpha_beta_double Density function of betabinomial with the shape parameterizations
dbetabinom_double The density function of the beta-binomial distribution.
dc_dtau Derivative of c = (1 - tau) / tau with respect to tau.
df_deps Derivative of f with respect to eps.
dlbeta_dc Derivative of the log-beta density with respect to c where c = (1 - tau)/tau where tau is the overdispersion parameter.
dlbeta_deps Derivative of the log-beta-binomial density with respect to the sequencing error rate.
dlbeta_dh Derivative of log-betabinomial density with respect to bias parameter.
dlbeta_dtau Derivative of the log-beta-binomial density with respect to the overdispersion parameter.
dlbeta_dxi Derivative of the log-betabinomial density with respect to the mean of the underlying beta.
doutdist The outlier distribution we use. Right now it is just a beta binomial with mean 1/2 and od 1/3 (so underlying beta is just a uniform from 0 to 1).
dpen_deps Derivative of -log(epsilon(1 - epsilon)) - (logit(epsilon) - mu_{epsilon})^2 / (2sigma_{epsilon}^2) with respect to epsilon.
dpen_dh Derivative of -log(h) - (log(h) - mu_h)^2 / (2sigma_h^2) with respect to h.
dr_pen Penalty used in 'update_dr'.
dxi_df Derivative of xi with respect to f.
dxi_dh Derivative of xi-function with respect to bias parameter.

-- E --

elbo The evidence lower bound
eta_double Adjusts allele dosage 'p' by the sequencing error rate 'eps'.
eta_fun Adjusts allele dosage 'p' by the sequencing error rate 'eps'.
expit The expit (logistic) function.

-- F --

f1_obj Objective for mixture of known dist and uniform dist.
flexdog Flexible genotyping for polyploids from next-generation sequencing data.
flexdog_full Flexible genotyping for polyploids from next-generation sequencing data.
flexdog_obj Log-likelihood that 'flexdog' maximizes.
flexdog_obj_out Log-likelihood that 'flexdog' maximizes when outliers are present.
flex_update_pivec Update the distribution of genotypes from various models.

-- G --

get_bivalent_probs Returns segregation probabilities, pairing representation and number of ref alleles given the ploidy.
get_bivalent_probs_dr Double reduction version of 'get_bivalent_probs'.
get_conv_inner_weights Get the inner weights used for the em update in 'update_pp_f1' when there are more than two bivalent components for one of the parents.
get_dimname Returns a vector character strings that are all of the possible combinations of the reference allele and the non-reference allele.
get_hyper_weights Return mixture weights needed to obtain a hypergeometric distribution.
get_inner_weights Compute inner weights for updating the mixing proportions when using ash model.
get_probk_vec Obtain the genotype distribution given the distribution of discrete uniforms.
get_q_array Return the probabilities of an offspring's genotype given its parental genotypes for all possible combinations of parental and offspring genotypes. This is for species with polysomal inheritance and bivalent, non-preferential pairing.
get_uni_rep Get the representation of a discrete unimodal probability distribution.
get_wik_mat E-step in 'flexdog'.
get_wik_mat_out E-step in 'flexdog' where we now allow an outlier distribution.
grad_for_eps Gradient for 'obj_for_eps'.
grad_for_mu_sigma2 Gradient for 'obj_for_mu_sigma2' with respect for 'mu' and 'sigma2'.
grad_for_mu_sigma2_wrapper Gradient for 'obj_for_mu_sigma2_wrapper' with respect for 'muSigma2' and a wrapper for 'grad_for_mu_sigma2'
grad_for_weighted_lbb Gradient for 'obj_for_weighted_lbb'.
grad_for_weighted_lnorm Gradient for 'obj_for_weighted_lnorm'.

-- I --

initialize_pivec Initialize 'pivec' for 'flexdog' EM algorithm.
is.flexdog Tests if an argument is a 'flexdog' object.
is.mupdog Tests if its argument is a mupdog object.

-- L --

logit The logit function.
log_sum_exp Log-sum-exponential trick.
log_sum_exp_2 Log-sum-exponential trick using just two doubles.

-- M --

mupdog Multi-SNP updog.
mupout A mupdog fit of the 'uitdewilligen' data.

-- O --

obj_for_alpha Objective function when updating alpha
obj_for_eps Objective function for updating sequencing error rate, bias, and overdispersion parameters.
obj_for_mu_sigma2 Objective function when updating mu and sigma2.
obj_for_mu_sigma2_wrapper Wrapper for 'obj_for_mu_sigma2' so that I can use it in 'optim'.
obj_for_rho Objective function when updating a single inbreeding coefficient.
obj_for_weighted_lbb Objective function for updating the beta-binomial genotype distribution when 'model = "bb"' in 'flex_update_pivec'.
obj_for_weighted_lnorm Objective funtion for updating discrete normal genotype distribution when 'model = "normal"' in 'flex_update_pivec'.
oracle_cor Calculates the correlation between the true genotype and an oracle estimator.
oracle_cor_from_joint Calculate the correlation of the oracle estimator with the true genotype from the joint distribution matrix.
oracle_joint The joint probability of the genotype and the genotype estimate of an oracle estimator.
oracle_mis Calculate oracle misclassification error rate.
oracle_mis_from_joint Get the oracle misclassification error rate directly from the joint distribution of the genotype and the oracle estimator.
oracle_mis_vec Returns the oracle misclassification rates for each genotype.
oracle_mis_vec_from_joint Get the oracle misclassification error rates (conditional on true genotype) directly from the joint distribution of the genotype and the oracle estimator.
oracle_plot Construct an oracle plot from the output of 'oracle_joint'.

-- P --

pbetabinom The Beta-Binomial Distribution
pbetabinom_double The distribution function of the betabinomial. This is generally only adviseable if q is relatively small.
pen_bias Penalty on bias parameter.
pen_seq_error Penalty on sequencing error rate.
pivec_from_segmats Function to get the segregation probabilities from the distributions of each component and the weights of each component.
plot.flexdog Draw a genotype plot from the output of 'flexdog'.
plot.mupdog Draw a genotype plot from the output of 'mupdog'.
plot_geno Make a genotype plot.
post_prob Variational posterior probability of having 'dosage' A alleles when the ploidy is 'ploidy', the allele frequency is 'alpha', the individual-specific overdispersion parameter is 'rho', the variational mean is 'mu', and the variational variance is 'sigma2'.
pp_brent_obj Objective function when doing Brent's method in 'update_pp_f1' when one parent only has two mixing components.

-- Q --

qbetabinom The Beta-Binomial Distribution
qbetabinom_double The quantile function of the beta-binomial distribution parameterized by mean and overdispersion parameter.

-- R --

rbetabinom The Beta-Binomial Distribution
rbetabinom_int One draw from the beta-binomial distribution parameterized by mean and overdispersion parameter.
rflexdog Simulate GBS data from the 'flexdog' likelihood.
rgeno Simulate individual genotypes from one of the supported 'flexdog' models.

-- S --

snpdat GBS data from Shirasawa et al (2017)
summary.mupdog Provides some summaries from the output of 'mupdog'.

-- U --

uitdewilligen Subset of individuals and SNPs from Uitdewilligen et al (2013).
uni_em EM algorithm to fit weighted ash objective.
uni_em_const EM algorithm to fit weighted ash objective with a uniform mixing component.
uni_obj Objective function optimized by 'uni_em'.
uni_obj_const Objective function optimized by 'uni_em_const'.
update_dr Same as 'update_pp_f1' but I exclusively use the EM (instead of also Brent's method), and I allow for priors on the mixing proportions.
update_pp_f1 Function to update the parameters in the preferential pairing F1 model.
update_pp_s1 Same as 'update_pp_f1' but only allow s1.
update_R Update the underlying correlation matrix.
updog 'updog' Flexible Genotyping for Polyploids

-- W --

wem Generalized version of 'uni_em'.

-- X --

xi_double Adjusts allele dosage 'p' by the sequencing error rate 'eps' and the allele bias 'h'.
xi_fun Adjusts allele dosage 'p' by the sequencing error rate 'eps' and the allele bias 'h'.