Man pages for deruncie/MegaLMM
MegaLMM
| bs_binomial_model | Sample Eta given B-splines individual-level model with... |
| bs_diff | B spline basis with option of centering and differencing... |
| cis_eQTL_model | Sample cis_eQTL coefficients |
| clear_Posterior | Resets Posterior samples |
| combined_model | Sample Eta given a list of different observation_models |
| create_data_matrices | Create data matrices for MegaLMM from a "tall" data.frame |
| estimate_memory_initialization_MegaLMM | Estimate the memory requirment for a fully initialized... |
| estimate_memory_posterior | Estimates the memory required to store a set of posterior... |
| find_candidate_states | Finds the set of variance component proportions within a... |
| get_posterior_FUN | Calculates the posterior mean of a function of parameters |
| get_posterior_HPDinterval | Calculates Highest Posteriod Density intervals of a function... |
| get_posterior_mean | Calculates posterior mean of a function of parameters |
| grapes-times-times-grapes | Multiply matrices |
| Image | Modification to 'image()'. |
| initialize_MegaLMM | Initialized Gibbs sampler for MegaLMM model |
| initialize_variables_MegaLMM | Initialize MegaLMM variables |
| K | Genomic Relationship matrix of 502 lines |
| load_posterior_param | load the posterior samples of a single parameter from all... |
| load_posterior_param_old | load the posterior samples of a single parameter from all... |
| matrix_multiply_toDense | Multiplies two matrices (sparse or dense by dense), returns... |
| MegaLMM_control | Set MegaLMM run parameters |
| MegaLMM_priors | Set MegaLMM priors |
| missing_data_model | Sample missing data |
| plot_diagnostics | Plots diagnostic plots for the fit of a MegaLMM model |
| plot.MegaLMM_state | Make plots of current MegaLMM state |
| print.MegaLMM_state | Print statistics on current MegaLMM state |
| regression_model | Sample Eta given regression-splines individual-level model |
| regression_sampler_parallel | Draws samples from all "fixed" coefficients (fixed and... |
| reload_Posterior | Re-loads a full Posterior list with all parameters |
| reorder_factors | Re-orders factors in decreasing order of magnitude |
| rstdnorm_mat | Draws a matrix of standard normal variables |
| sample_MegaLMM | Run MegaLMM Gibbs sampler |
| save_posterior_chunk | Saves a chunk of posterior samples |
| save_posterior_sample | Saves current state in Posterior |
| set_priors_MegaLMM | Set priors for MegaLMM model. |
| setup_model_MegaLMM | Set up a MegaLMM model |
| SingleSite_regression_sampler_parallel | Draws samples from all "fixed" coefficients (fixed and... |
| summary.MegaLMM_state | Print more detailed statistics on current MegaLMM state |
| toDense | Converts dense Matrix to "matrix" faster! |
| traceplot_array | Make a trace plot of a set of related parameters from MegaLMM |
| voom_model | Sample Eta given a voom observation model |
| yield_data | Yield BLUPs for 502 lines across 19 trials |
