Methods for Adaptive Shrinkage, using Empirical Bayes

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Documentation for package ‘ashr’ version 2.0.5

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ashr-package ashr
ash Main Adaptive Shrinkage function
ash.workhorse Detailed Adaptive Shrinkage function
ashci Credible Interval Computation for the ash object
ashr ashr
calc_loglik Compute loglikelihood for data from ash fit
calc_logLR Compute loglikelihood ratio for data from ash fit
calc_mixmean Generic function of calculating the overall mean of the mixture
calc_mixsd Generic function of calculating the overall standard deviation of the mixture
calc_null_loglik Compute loglikelihood for data under null that all beta are 0
calc_null_vloglik Compute vector of loglikelihood for data under null that all beta are 0
calc_vloglik Compute vector of loglikelihood for data from ash fit
calc_vlogLR Compute vector of loglikelihood ratio for data from ash fit
cdf.ash cdf method for ash object
cdf_post cdf_post
compute_lfsr Function to compute the local false sign rate
comp_cdf Generic function of computing the cdf for each component
comp_cdf_post comp_cdf_post
comp_dens Generic function of calculating the component densities of the mixture
comp_dens_conv comp_dens_conv
comp_dens_conv.normalmix comp_dens_conv.normalmix
comp_dens_conv.unimix density of convolution of each component of a unif mixture
comp_mean Generic function of calculating the first moment of components of the mixture
comp_mean.normalmix comp_mean.normalmix
comp_mean2 Generic function of calculating the second moment of components of the mixture
comp_postmean comp_postmean
comp_postmean2 comp_postmean2
comp_postprob comp_postprob
comp_postsd comp_postsd
comp_sd Generic function to extract the standard deviations of components of the mixture
comp_sd.normalmix comp_sd.normalmix
dens Find density at y, a generic function
dens_conv dens_conv
dlogf The log-F distribution
estimate_mixprop Estimate mixture proportions of a mixture g given noisy (error-prone) data from that mixture.
gen_etruncFUN gen_etruncFUN
get_density Density method for ash object
get_fitted_g Return lfsr, lfdr, etc from ash object
get_lfdr Return lfsr, lfdr, etc from ash object
get_lfsr Return lfsr, lfdr, etc from ash object
get_loglik Return lfsr, lfdr, etc from ash object
get_logLR Return lfsr, lfdr, etc from ash object
get_np Return lfsr, lfdr, etc from ash object
get_pi0 Return lfsr, lfdr, etc from ash object
get_pm Return lfsr, lfdr, etc from ash object
get_pp Return lfsr, lfdr, etc from ash object
get_psd Return lfsr, lfdr, etc from ash object
get_qvalue Return lfsr, lfdr, etc from ash object
get_svalue Return lfsr, lfdr, etc from ash object
igmix Constructor for igmix class
logF_lik Likelihood object for logF error distribution
loglik_conv loglik_conv
loglik_conv.default loglik_conv.default
log_comp_dens_conv log_comp_dens_conv
log_comp_dens_conv.normalmix log_comp_dens_conv.normalmix
log_comp_dens_conv.unimix log density of convolution of each component of a unif mixture
mixcdf mixcdf
mixcdf.default mixcdf.default
mixEM Estimate mixture proportions of a mixture model by EM algorithm
mixIP Estimate mixture proportions of a mixture model by Interior Point method
mixmean2 Generic function of calculating the overall second moment of the mixture
mixprop Generic function of extracting the mixture proportions
mixVBEM Estimate posterior distribution on mixture proportions of a mixture model by a Variational Bayes EM algorithm
my_e2truncnorm More about the truncated normal
my_e2trunct my_e2trunct
my_etrunclogf my_etrunclogf
my_etruncnorm my_etruncnorm
my_etrunct my_etrunct
my_vtruncnorm This version is better than trunvnorm package
ncomp ncomp
ncomp.default ncomp.default
normalmix Constructor for normalmix class
normal_lik Likelihood object for normal error distribution
pcdf_post pcdf_post
plogf The log-F distribution
plot.ash Plot method for ash object
pm_on_zero Generic function to extract which components of mixture are point mass on 0
posterior_dist Compute Posterior
postmean postmean
postmean2 postmean2
postsd postsd
print.ash Print method for ash object
qval.from.lfdr Function to compute q values from local false discovery rates
set_data Takes raw data and sets up data object for use by ash
summary.ash Summary method for ash object
t_lik Likelihood object for t error distribution
unimix Constructor for unimix class
vcdf_post vcdf_post