Man pages for stephenslab/mashr
Multivariate Adaptive Shrinkage

calc_lik_matrixCompute matrix of conditional likelihoods.
calc_lik_matrix_common_covcalc_lik_matrix_common_cov
calc_lik_vectorCompute conditional likelihoods for bhat vector.
calc_relative_lik_matrixCalculate matrix of relative likelihoods.
compute_alt_loglik_from_matrix_and_piCompute vector of alternative loglikelihoods from a matrix of...
compute_loglik_from_matrix_and_piCompute total loglikelihood from a matrix of log-likelihoods...
compute_null_correlation_lower_boundcompute_null_correlation_lower_bound
compute_posterior_matricesCompute posterior matrices.
compute_posterior_matrices_common_cov_RCompute posterior matrices (when error covariance V_j is...
compute_posterior_matrices_general_RCompute posterior matrices (general version)
compute_posterior_weightscompute posterior probabilities
compute_vloglik_from_matrix_and_piCompute vector of loglikelihoods from a matrix of...
cov_all_zerosCompute an R by R matrix of all 0s
cov_canonicalCompute a list of canonical covariance matrices
cov_edPerform "extreme deconvolution" (Bovy et al) on a subset of...
cov_equal_effectsCompute an R by R matrix of all 1s
cov_first_singletonCompute all the singleton matrices corresponding to...
cov_from_factorsproduce list of rank 1 covariance matrices corresponding to...
cov_pcaPerform PCA on data and return list of candidate covariance...
cov_simple_hetCompute covariance matrices with diagonal element 1 and...
cov_udiCompute a list of covariance matrices corresponding to the...
cov_udi_singlecomputes the covariance matrix for a single UDI model
ed_wrapperFit extreme deconvolution to mash data
estimate_null_correlationEstimate null correlations
expand_covCreate expanded list of covariance matrices expanded by grid,...
get_estimated_piReturn the estimated mixture proportions
get_log10bfReturn the Bayes Factor for each effect
get_n_significant_conditionsCount number of conditions each effect is significant in
get_pairwise_sharingCompute the proportion of (significant) signals shared by...
get_significant_resultsFind effects that are significant in at least one condition
initialize_piInitialize mixture proportions - currently by making them all...
is_common_covCheck that all covariates are equal.
make_namesCreate names for covariance matrices
mashApply mash method to data
mash_1by1Perform condition-by-condition analyses
mash_compute_loglikCompute loglikelihood for fitted mash object on new data
mash_compute_posterior_matricesCompute posterior matrices for fitted mash object on new data
mash_compute_vloglikCompute vector of loglikelihood for fitted mash object on new...
mash_plot_metaPlot metaplot for an effect based on posterior from mash
optimize_piEstimate the mixture weights by maximum (penalized)...
posterior_covposterior_cov
posterior_meanposterior_mean
posterior_mean_matrixposterior_mean_matrix
scale_covScale each covariance matrix in list Ulist by a scalar in...
set_mash_dataCreate a data object for mash analysis
simple_simsCreate some simple simulated data for testing purposes
simple_sims2Create some more simple simulated data for testing purposes
udi_model_matrixCreate a matrix whose rows contain all possible combinations...
stephenslab/mashr documentation built on Oct. 9, 2017, 5:31 a.m.