# Man pages for mashrMultivariate Adaptive Shrinkage

 bovy_wrapper Fit extreme deconvolution to mash data using Bovy et al 2011 calc_lik_matrix Compute matrix of conditional likelihoods. calc_lik_matrix_common_cov calc_lik_matrix_common_cov calc_lik_vector Compute conditional likelihoods for bhat vector. calc_relative_lik_matrix Calculate matrix of relative likelihoods. compute_alt_loglik_from_matrix_and_pi Compute vector of alternative loglikelihoods from a matrix of... compute_loglik_from_matrix_and_pi Compute the total loglikelihood from a matrix of... compute_null_loglik_from_matrix Compute a vector of null loglikelihoods from a matrix of... compute_posterior_matrices Compute posterior matrices. compute_posterior_matrices_common_cov_R Compute posterior matrices (when error covariance V_j is... compute_posterior_matrices_general_R Compute posterior matrices (general version) compute_posterior_weights Compute posterior probabilities that each effect came from... compute_vloglik_from_matrix_and_pi Computes a vector of loglikelihoods from a matrix of... contrast_matrix Create contrast matrix cov_all_zeros Compute an R by R matrix of all 0s cov_canonical Compute a list of canonical covariance matrices cov_ed Perform "extreme deconvolution" (Bovy et al) on a subset of... cov_equal_effects Compute an R by R matrix of all 1s cov_first_singleton Compute all the singleton matrices corresponding to... cov_flash Perform Empirical Bayes Matrix Factorization via FLASH and... cov_from_factors produce list of rank-1 covariance matrices corresponding to... cov_pca Perform PCA on data and return list of candidate covariance... cov_simple_het Compute covariance matrices with diagonal element 1 and... cov_udi Compute a list of covariance matrices corresponding to the... cov_udi_single Computes the covariance matrix for a single UDI model estimate_null_correlation Estimate null correlations estimate_null_correlation_simple Estimate null correlations (simple) expand_cov Create expanded list of covariance matrices expanded by grid,... extreme_deconvolution Density estimation using Gaussian mixtures in the presence of... get_estimated_pi Return the estimated mixture proportions get_log10bf Return the Bayes Factor for each effect get_n_significant_conditions Count number of conditions each effect is significant in get_pairwise_sharing Compute the proportion of (significant) signals shared by... get_pairwise_sharing_from_samples Compute the proportion of (significant) signals shared by... get_samples Return samples from a mash object get_significant_results Find effects that are significant in at least one condition make_names Create names for covariance matrices mash Apply mash method to data mash_1by1 Perform condition-by-condition analyses mash_compute_loglik Compute loglikelihood for fitted mash object on new data. mash_compute_posterior_matrices Compute posterior matrices for fitted mash object on new data mash_compute_vloglik Compute vector of loglikelihood for fitted mash object on new... mash_plot_meta Plot metaplot for an effect based on posterior from mash mash_set_data Create a data object for mash analysis. mash_set_data_contrast Create a data object for mash contrast analysis mash_update_data Update the data object for mash analysis. optimize_pi Estimate mixture weights by maximum (penalized) likelihood posterior_cov posterior_cov posterior_mean posterior_mean posterior_mean_matrix posterior_mean_matrix scale_cov Scale each covariance matrix in list Ulist by a scalar in... sim_contrast1 Create simplest simulation, cj = mu 1 data used for contrast... sim_contrast2 Create simulation with signal data used for contrast... simple_sims Create some simple simulated data for testing purposes simple_sims2 Create some more simple simulated data for testing purposes teem_wrapper Fit extreme deconvolution to mash data using TEEM method... udi_model_matrix Create a matrix whose rows contain all possible combinations...
mashr documentation built on May 24, 2021, 1:06 a.m.