Man pages for mashr
Multivariate 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 using flashier,... |
| 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_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_estimate_corr_em | Fit mash model and estimate residual correlations using EM... |
| 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... |
