# Man pages for stephenslab/mashrMultivariate Adaptive Shrinkage

 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 total loglikelihood from a matrix of log-likelihoods... compute_null_correlation_lower_bound compute_null_correlation_lower_bound compute_null_loglik_from_matrix Compute 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 compute_vloglik_from_matrix_and_pi Compute vector of loglikelihoods from a matrix of... 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_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 ed_wrapper Fit extreme deconvolution to mash data estimate_null_correlation Estimate null correlations expand_cov Create expanded list of covariance matrices expanded by grid,... 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_significant_results Find effects that are significant in at least one condition initialize_pi Initialize mixture proportions - currently by making them all... is_common_cov_Shat Check that all covariances are equal (Shat). is_common_cov_Shat_alpha Check that all rows of Shat_alpha are the same. 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 optimize_pi Estimate the mixture weights by maximum (penalized)... 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 udi_model_matrix Create a matrix whose rows contain all possible combinations...
stephenslab/mashr documentation built on Oct. 16, 2018, 9:12 p.m.