Man pages for ashr
Methods for Adaptive Shrinkage, using Empirical Bayes
| ash | Adaptive Shrinkage |
| ashci | Credible Interval Computation for the ash object |
| ash_pois | Performs adaptive shrinkage on Poisson data |
| 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... |
| calc_mixsd | Generic function of calculating the overall standard... |
| 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... |
| 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_conv | cdf_conv |
| cdf_post | cdf_post |
| comp_cdf | Generic function of computing the cdf for each component |
| comp_cdf_conv | comp_cdf_conv |
| comp_cdf_conv.normalmix | comp_cdf_conv.normalmix |
| comp_cdf_conv.unimix | cdf of convolution of each component of a unif mixture |
| comp_cdf_post | comp_cdf_post |
| comp_dens | Generic function of calculating the component densities of... |
| 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... |
| comp_mean2 | Generic function of calculating the second moment of... |
| comp_mean.normalmix | comp_mean.normalmix |
| comp_mean.tnormalmix | comp_mean.tnormalmix |
| 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... |
| comp_sd.normalmix | comp_sd.normalmix |
| comp_sd.tnormalmix | comp_sd.normalmix |
| compute_lfsr | Function to compute the local false sign rate |
| cxxMixSquarem | Brief description of function. |
| 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... |
| gen_etruncFUN | gen_etruncFUN |
| get_density | Density method for ash object |
| get_lfdr | Return lfsr from an ash object |
| get_post_sample | Sample from posterior |
| igmix | Constructor for igmix class |
| lik_binom | Likelihood object for Binomial error distribution |
| lik_logF | Likelihood object for logF error distribution |
| lik_normal | Likelihood object for normal error distribution |
| lik_normalmix | Likelihood object for normal mixture error distribution |
| lik_pois | Likelihood object for Poisson error distribution |
| lik_t | Likelihood object for t error distribution |
| 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... |
| loglik_conv | loglik_conv |
| loglik_conv.default | loglik_conv.default |
| mixcdf | mixcdf |
| mixcdf.default | mixcdf.default |
| mixEM | Estimate mixture proportions of a mixture model by EM... |
| mixIP | Estimate mixture proportions of a mixture model by Interior... |
| mixmean2 | Generic function of calculating the overall second moment of... |
| mixprop | Generic function of extracting the mixture proportions |
| mixSQP | Estimate mixture proportions of a mixture model using mix-SQP... |
| mixVBEM | Estimate posterior distribution on mixture proportions of a... |
| my_e2truncbeta | second moment of truncated Beta distribution |
| my_e2truncgamma | second moment of truncated gamma distribution |
| my_e2truncnorm | Expected Squared Value of Truncated Normal |
| my_e2trunct | my_e2trunct |
| my_etruncbeta | mean of truncated Beta distribution |
| my_etruncgamma | mean of truncated gamma distribution |
| my_etrunclogf | my_etrunclogf |
| my_etruncnorm | Expected Value of Truncated Normal |
| my_etrunct | my_etrunct |
| my_vtruncnorm | Variance of Truncated Normal |
| ncomp | ncomp |
| ncomp.default | ncomp.default |
| normalmix | Constructor for normalmix class |
| pcdf_post | pcdf_post |
| plogf | The log-F distribution |
| plot.ash | Plot method for ash object |
| plot_diagnostic | Diagnostic plots for ash object |
| pm_on_zero | Generic function to extract which components of mixture are... |
| posterior_dist | Compute Posterior |
| postmean | postmean |
| postmean2 | postmean2 |
| post_sample | post_sample |
| post_sample.normalmix | post_sample.normalmix |
| post_sample.unimix | post_sample.unimix |
| postsd | postsd |
| print.ash | Print method for ash object |
| prune | prune |
| 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 |
| tnormalmix | Constructor for tnormalmix class |
| unimix | Constructor for unimix class |
| vcdf_post | vcdf_post |
| w_mixEM | Estimate mixture proportions of a mixture model by EM... |
