scristia/CNPBayes
Bayesian mixture models for copy number polymorphisms

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Source code
49
Man pages
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scristia/CNPBayes: Bayesian mixture models for copy number polymorphisms
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API for scristia/CNPBayes
Bayesian mixture models for copy number polymorphisms

Global functions
"[",MixtureModel,logical,ANY,ANY Man page
"[",MixtureModel,numeric,ANY,ANY Man page
"[",MultiBatchModel,ANY,ANY,ANY Man page
"[[",MultiBatchList,numeric,ANY Man page
.blockUpdatesBatch Source code
.blockUpdatesMultiBatchPooled Source code
.combineBatches Source code
.computeProbZ Source code
.empty_batch_model Source code
.gg_multibatch Source code
.gg_multibatch_copynumber Source code
.gg_multibatch_pooled Source code
.init_kmeans Source code
.init_priors Source code
.init_sb1 Source code
.initializeMcmc Source code
.initializeMcmcBatch Source code
.initializeMcmcPooledVar Source code
.initialize_z Source code
.initialize_z_singlebatch Source code
.ml_batchmodel Source code
.ml_list Source code
.ml_multibatch_pooled Source code
.modelProb Source code
.ordered_thetas_multibatch Source code
.pBAF_012 Source code
.pBAF_12 Source code
.p_b Source code
.param_updates Source code
.parameterizeGammaByMeanSd Source code
.posteriorSimulation2 Source code
.predictiveDataTable Source code
.read_hapmap Source code
.sigma2_batch Source code
.testcnp Source code
CNPBayes Man page
Hyperparameters Man page Source code
Hyperparameters-class Man page
HyperparametersMultiBatch Man page Source code
HyperparametersMultiBatch-class Man page
HyperparametersSingleBatch Man page Source code
HyperparametersSingleBatch-class Man page
HyperparametersTrios-class Man page
McmcChains-class Man page
McmcParams Man page Source code
McmcParams-class Man page
MixtureModel-class Man page
MultiBatch Man page Source code
MultiBatch-class Man page
MultiBatchList Man page Source code
MultiBatchModel-class Man page
MultiBatchModelExample Man page
MultiBatchP Source code
MultiBatchPooledExample Man page
SB Source code
SingleBatchCopyNumber-class Man page
SingleBatchModel-class Man page
SingleBatchModel2 Source code
SingleBatchModelExample Man page
SingleBatchPooled Source code
[,McmcChains,ANY,ANY,ANY-method Man page
[,McmcChains,ANY-method Man page
[,McmcChains-method Man page
[,MixtureModel,logical,ANY,ANY-method Man page
[,MixtureModel,numeric,ANY,ANY-method Man page
[,MultiBatch,logical,ANY,ANY-method Man page
[,MultiBatch,numeric,ANY,ANY-method Man page
[,MultiBatchList,ANY,ANY,ANY Man page
[,MultiBatchList,character,ANY,ANY Man page
[,MultiBatchList,character,ANY,ANY-method Man page
[,MultiBatchList,logical,ANY,ANY Man page
[,MultiBatchList,logical,ANY,ANY-method Man page
[,MultiBatchList,numeric,ANY,ANY Man page
[,MultiBatchList,numeric,ANY,ANY-method Man page
[,MultiBatchModel,ANY,ANY,ANY-method Man page
[<-,MultiBatchList,ANY,ANY,ANY-method Man page
[[,CnList,numeric,ANY-method Man page
[[,MultiBatchList,character,ANY Man page
[[,MultiBatchList,character,ANY-method Man page
[[,MultiBatchList,numeric,ANY-method Man page
[[<-,MultiBatchList,ANY,ANY Man page
[[<-,MultiBatchList,ANY,ANY,ANY-method Man page
[[<-,MultiBatchList,ANY,ANY-method Man page
a Source code
aa Source code
aaab Source code
aab Source code
ab Source code
abb Source code
abbb Source code
annotateRegions Source code
anyWarnings Source code
argMax Source code
b Source code
bafLikelihood Man page Source code
bafs Source code
batch Man page
batch,MixtureModel-method Man page
batch,MultiBatch-method Man page
batch,MultiBatchList-method Man page
bayesFactor Man page
bb Source code
betas Source code
bic Man page
bic,MultiBatch-method Man page
bic,MultiBatchModel-method Man page
bic,MultiBatchP-method Man page
bic,MultiBatchPooled-method Man page
blockUpdates Source code
burnin Man page
burnin,McmcParams-method Man page
burnin,MixtureModel-method Man page
burnin,MultiBatch-method Man page
burnin,MultiBatchList-method Man page
burnin<- Man page
burnin<-,McmcParams,ANY-method Man page
burnin<-,McmcParams-method Man page
burnin<-,MixtureModel,ANY-method Man page
burnin<-,MultiBatch,numeric-method Man page
burnin<-,MultiBatchList,numeric-method Man page
burnin_multibatch_pvar Source code
burnin_nomendelian_update Source code
candidateModels Source code
ccmap Source code
chains Man page
chains,MixtureModel-method Man page
chains,MultiBatch-method Man page
chains,MultiBatchList-method Man page
chains_mb Source code
cmap Source code
cnv_models Man page
combine_singlebatch_pooled Source code
compute_heavy_means Source code
compute_heavy_means_batch Source code
compute_heavy_sums Source code
compute_heavy_sums_batch Source code
compute_loglik Source code
compute_logprior Source code
compute_means Source code
compute_prec Source code
compute_prec2 Source code
compute_u_sums Source code
compute_u_sums_batch Source code
compute_vars Source code
compute_vars2 Source code
consensusCNP Man page Source code
consensusRegion Source code
cpp_burnin Source code
cpp_mcmc Source code
cumProbs Source code
d1 Source code
d2 Source code
d3 Source code
d4 Source code
d_beta Source code
defineCnpRegions Source code
dlocScale_t Source code
down_sample2 Man page
effectiveSizeWarning Source code
extractFromModelList Source code
extractParameters Source code
failEffectiveSize Source code
family_member Source code
findSurrogates,MultiBatch-method Man page
fitModelK Source code
fit_restricted2 Man page
gelmanDiag Source code
genotype_model Man page
genotypes Source code
getDf Source code
getK Source code Source code
ggMixture Man page
ggMixture,MultiBatch-method Man page
ggMixture,MultiBatchCopyNumber-method Man page
ggMixture,MultiBatchCopyNumberPooled-method Man page
ggMixture,MultiBatchModel-method Man page
ggMixture,MultiBatchPooled-method Man page
harmonizeDimensions Source code
hemdel_model Man page
homdel_model Man page
homdeldup_model Man page
hpList Source code
hyperParamList Source code
hyperParams Man page
hyperParams,MixtureModel-method Man page
hyperParams,MultiBatch-method Man page
hyperParams,MultiBatchList-method Man page
hyperParams<- Man page
hyperParams<-,MixtureModel,Hyperparameters-method Man page
hyperParams<-,MultiBatch,Hyperparameters-method Man page
hyperParams<-,MultiBatchList,Hyperparameters-method Man page
id Man page
id,MultiBatch-method Man page
id,MultiBatchList-method Man page
initialize_mcmc Source code
initialize_mcmcP Source code
initialize_mcmcT Source code
integerMatrix Source code
isSimulated Man page
isSimulated,MixtureModel-method Man page
isSimulated,MultiBatch-method Man page
isSimulated,MultiBatchList-method Man page
is_child Source code
is_father Source code
is_mother Source code
is_parent Source code
iter Man page
iter,McmcChains-method Man page
iter,McmcParams-method Man page
iter,MixtureModel-method Man page
iter,MultiBatch-method Man page
iter,MultiBatchList-method Man page
iter,burnin,nStarts,McmcParams-method Man page
iter<- Man page
iter<-,McmcChains,ANY-method Man page
iter<-,McmcParams,ANY-method Man page
iter<-,MixtureModel,ANY-method Man page
iter<-,MultiBatch,numeric-method Man page
iter<-,MultiBatchList,numeric-method Man page
k Man page
k,Hyperparameters-method Man page
k,McmcChains-method Man page
k,MixtureModel-method Man page
k,MultiBatch-method Man page
k,MultiBatchList-method Man page
k<- Man page
k<-,Hyperparameters-method Man page
k<-,MultiBatchList,ANY-method Man page
kolmogorov_batches Man page
length,CnList-method Man page
length,MultiBatchList-method Man page
listChains1 Source code
listChains2 Source code
listFlags Source code
listSummaries Source code
listToMultiBatchList Source code
listValues Source code
logBayesFactor Source code
logLikc Source code
log_ddirichlet_ Source code
log_lik Man page
log_lik,McmcChains-method Man page
log_lik,MixtureModel-method Man page
log_lik,MultiBatch-method Man page
log_prob_mu Source code
log_prob_nu0 Source code
log_prob_nu0p Source code
log_prob_pmix Source code
log_prob_pmix2 Source code
log_prob_s20 Source code
log_prob_s20p Source code
log_prob_sigma2 Source code
log_prob_sigmap Source code
log_prob_tau2 Source code
log_prob_theta Source code
log_prob_thetap Source code
loglik_multibatch_pvar Source code
longFormatKB Source code
lookup_mprobs Source code
makeUnique Source code
mapCnProbability Source code
mapModel Source code
map_z Man page Source code
mapping Man page
mapping,MultiBatch-method Man page
mapping<- Man page
mapping<-,MultiBatch-method Man page
marginalLik Man page
marginalLikelihood Man page
marginalLikelihood,MultiBatchModel,ANY-method Man page
marginalLikelihood,MultiBatchModel-method Man page
marginalLikelihood,MultiBatchPooled-method Man page
marginalLikelihood,list,ANY-method Man page
marginalLikelihood,list-method Man page
marginal_lik Man page
marginal_lik,MixtureModel-method Man page
marginal_lik,MultiBatch-method Man page
marginal_lik,MultiBatchList-method Man page
marginal_lik<- Man page
marginal_lik<-,MixtureModel,numeric-method Man page
marginal_lik<-,MultiBatch,numeric-method Man page
marginal_theta_batch Source code
marginal_theta_pooled Source code
mb_homozygous_burnin Source code
mb_homozygous_mcmc Source code
mb_pred_data Source code
mb_predictive Source code
mbp_homozygous_burnin Source code
mbp_homozygous_mcmc Source code
mcmc3 Source code
mcmcParams Man page
mcmcParams,MixtureModel-method Man page
mcmcParams,MultiBatch-method Man page
mcmcParams,MultiBatchList-method Man page
mcmcParams,list-method Man page
mcmcParams<- Man page
mcmcParams<-,MixtureModel,ANY-method Man page
mcmcParams<-,MultiBatch,McmcParams-method Man page
mcmcParams<-,MultiBatchList,McmcParams-method Man page
mcmcParams<-,MultiBatchP,McmcParams-method Man page
mcmcParams<-,list,ANY-method Man page
mcmcWithHomDel Man page
mcmc_chains Source code
mcmc_chainsP Source code
mcmc_multibatch_pvar Source code
mcmc_nomendelian_update Source code
median_summary Man page
missingBatch Source code
mixtureProbs Source code
mixture_layout Man page
mixture_plot Man page
mlParams Source code
modelName Man page
modelName,MixtureModel-method Man page
modelName,MultiBatch-method Man page
modelName,MultiBatchList-method Man page
modelParameters Source code
modelProb Source code
modelSpecs Source code
modelSummariesP Source code
modelValues2 Source code
modelValuesP Source code
model_spec Source code
mu,McmcChains-method Man page
muMean Source code
muc Source code
multibatch_figure Source code
multinomialPr_multibatch_pvar Source code
nComp Source code
nStarts Man page
nStarts,McmcParams-method Man page
nStarts<- Man page
nStarts<-,McmcParams,ANY-method Man page
nStarts<-,McmcParams-method Man page
names,McmcChains-method Man page
names,MultiBatchList-method Man page
ntile Source code
nu.0 Man page
nu.0,McmcChains-method Man page
nu0_multibatch_pvar Source code
nu0c Source code
null Source code
numberObs Man page
numberObs,MixtureModel-method Man page
observed Source code
oned Man page
oned,MixtureModel-method Man page
oned,MultiBatch-method Man page
oned,MultiBatchList-method Man page
orderModels Man page
pBAF_012 Source code
pBAF_0123 Source code
pBAF_01234 Source code
pBAF_02 Source code
pBAF_12 Source code
pBAF_123 Source code
pBAF_2 Source code
pBAF_23 Source code
pBAF_234 Source code
pBaf Source code
p_b Source code
p_outlier Source code
permnK Source code
pic Source code
posteriorSimulation Man page
posteriorSimulation,MixtureModel-method Man page
posteriorSimulation,MultiBatch-method Man page
posteriorSimulation,MultiBatchList-method Man page
posteriorSimulation,MultiBatchP-method Man page
posteriorSimulation,TrioBatchModel-method Man page
posteriorSimulation,list-method Man page
posteriorSimulationNoMendel Source code
posteriorSimulationPooled Source code
predictiveTibble Source code
predictive_trios Source code
prob_mendelian Source code
probz Man page
probz,MixtureModel-method Man page
probz,MultiBatch-method Man page
psParams Source code
qInverseTau2 Source code
rMultinom Source code
readLocalHapmap Source code
reduced_mu_batch Source code
reduced_mu_pooled Source code
reduced_nu0_batch Source code
reduced_nu0_pooled Source code
reduced_pi_batch2 Source code
reduced_pi_pooled Source code
reduced_pi_pooled2 Source code
reduced_s20_batch Source code
reduced_sigma_batch Source code
reduced_sigma_pooled Source code
reduced_tau2_pooled Source code
reduced_tau_batch Source code
reorderMultiBatch Source code
reorderMultiBatchPooled Source code
restartAtChainIndex Source code
revertToMultiBatch Man page
rlocScale_t Source code
sample_components Source code
sample_componentsP Source code
sample_trio_components Source code
saveBatch Source code
sb_pred_data Source code
sb_predictive Source code
selectByLogLik Source code
shapeParams Source code
sigma Source code
sigma.0 Source code
sigma2 Man page
sigma2,McmcChains-method Man page
sigma2,MixtureModel-method Man page
sigma2,MultiBatch-method Man page
sigma2,MultiBatchCopyNumberPooled-method Man page
sigma2,MultiBatchPooled-method Man page
sigma2,missing-method Man page
sigma2.0 Man page
sigma2.0,McmcChains-method Man page
sigma20_multibatch_pvar Source code
sigma20c Source code
sigma2_multibatch_pvar Source code
sigmac Source code
simulateBatchData Man page Source code
simulateData Man page Source code
simulateThetas Source code
simulateZ Source code
smallPlates Source code
stageTwoLogLikBatch Source code
stagetwo_multibatch_pvar Source code
startAtTrueValues Source code
summarize_region Man page
tableBatchZ Source code
tableBatchZpar Source code
tableZ Source code
tableZpar Source code
tau Source code
tau.0 Source code
tau2,McmcChains-method Man page
tau2Hyperparams Source code
tau2HyperparamsBatch Source code
tauMean Source code
tauc Source code
test_trio Source code
theta Man page
theta,McmcChains-method Man page
theta,MixtureModel-method Man page
theta,MultiBatch-method Man page
theta<- Man page
theta<-,McmcChains,ANY-method Man page
theta<-,MixtureModel,ANY-method Man page
theta<-,MultiBatch,matrix-method Man page
theta<-,MultiBatchModel,ANY-method Man page
thetaEffectiveSize Source code
theta_multibatch_pvar Source code
thin Man page
thin,McmcParams-method Man page
thin,MixtureModel-method Man page
thin,MultiBatch-method Man page
thin,MultiBatchList-method Man page
thin<- Man page
thin<-,McmcParams,numeric-method Man page
thin<-,MixtureModel,numeric-method Man page
thin<-,MultiBatch,numeric-method Man page
thin<-,MultiBatchList,numeric-method Man page
tileSummaries Source code
trios_burnin Source code
trios_mcmc Source code
unique_batch Source code
upSample2 Source code
update_mendel_prob Source code
update_mendelian Source code
update_mu Source code
update_mu2 Source code
update_multinomialPr Source code
update_multinomialPrChild Source code
update_multinomialPrPar Source code
update_nu0 Source code
update_offspring Source code
update_p Source code
update_parents Source code
update_pp Source code
update_predictive Source code
update_predictiveP Source code
update_probz Source code
update_probzpar Source code
update_sigma2 Source code
update_sigma20 Source code
update_sigma22 Source code
update_tau2 Source code
update_theta Source code
update_trioPr Source code
update_trioPr2 Source code
update_weightedp Source code
update_z Source code
update_z2 Source code
update_zchild Source code
update_zparents Source code
upsample2 Man page
useSingleBatchValues Source code
warmup Man page
z Man page
z,MixtureModel-method Man page
z,MultiBatch-method Man page
z2cn Source code
zFreq,McmcChains-method Man page
z_multibatch_pvar Source code
zfreq,McmcChains-method Man page
scristia/CNPBayes documentation built on Aug. 9, 2020, 7:31 p.m.

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