ashr

Adaptive Shrinkage

Performs adaptive shrinkage on Poisson data

Credible Interval Computation for the ash object

ashr

Compute loglikelihood ratio for data from ash fit

Compute loglikelihood for data from ash fit

Generic function of calculating the overall mean of the mixture

Generic function of calculating the overall standard deviation of the mixture

Compute loglikelihood for data under null that all beta are 0

Compute vector of loglikelihood for data under null that all beta are 0

Compute vector of loglikelihood ratio for data from ash fit

Compute vector of loglikelihood for data from ash fit

cdf method for ash object

cdf_conv

cdf_post

Generic function of computing the cdf for each component

comp_cdf_conv

comp_cdf_conv.normalmix

cdf of convolution of each component of a unif mixture

comp_cdf_post

Generic function of calculating the component densities of the mixture

comp_dens_conv

comp_dens_conv.normalmix

density of convolution of each component of a unif mixture

Generic function of calculating the first moment of components of the mixture

comp_mean.normalmix

Generic function of calculating the second moment of components of the mixture

comp_postmean

comp_postmean2

comp_postprob

comp_postsd

Generic function to extract the standard deviations of components of the mixture

comp_sd.normalmix

Function to compute the local false sign rate

Brief description of function.

Find density at y, a generic function

dens_conv

The log-F distribution

Estimate mixture proportions of a mixture g given noisy (error-prone) data from that mixture.

gen_etruncFUN

Density method for ash object

Return lfsr from an ash object

Sample from posterior

Constructor for igmix class

Likelihood object for Binomial error distribution

Likelihood object for logF error distribution

Likelihood object for normal error distribution

Likelihood object for normal mixture error distribution

Likelihood object for Poisson error distribution

Likelihood object for t error distribution

log_comp_dens_conv

log_comp_dens_conv.normalmix

log density of convolution of each component of a unif mixture

loglik_conv

loglik_conv.default

Estimate mixture proportions of a mixture model by EM algorithm

Estimate mixture proportions of a mixture model by Interior Point method

Estimate mixture proportions of a mixture model using mix-SQP algorithm.

Estimate posterior distribution on mixture proportions of a mixture model by a Variational Bayes EM algorithm

mixcdf

mixcdf.default

Generic function of calculating the overall second moment of the mixture

Generic function of extracting the mixture proportions

second moment of truncated Beta distribution

second moment of truncated gamma distribution

Expected Squared Value of Truncated Normal

my_e2trunct

mean of truncated Beta distribution

mean of truncated gamma distribution

my_etrunclogf

Expected Value of Truncated Normal

my_etrunct

Variance of Truncated Normal

ncomp

ncomp.default

Constructor for normalmix class

pcdf_post

The log-F distribution

Plot method for ash object

Diagnostic plots for ash object

Generic function to extract which components of mixture are point mass on 0

post_sample

post_sample.normalmix

post_sample.unimix

Compute Posterior

postmean

postmean2

postsd

Print method for ash object

prune

Function to compute q values from local false discovery rates

Takes raw data and sets up data object for use by ash

Summary method for ash object

Constructor for unimix class

vcdf_post

Estimate mixture proportions of a mixture model by EM algorithm (weighted version)