Man pages for dcgerard/vicar
Various Ideas for Confounder Adjustment in Regression
| adjust_by_t | Returns adjusted sebetahat's based on t likelihood so that we... |
| ash_ruv2 | Use control genes to estimate hidden confounders and variance... |
| ash_ruv4 | Use control genes to estimate hidden confounders and variance... |
| ash_wrap | Wrapper for 'ash.workhorse' for use in 'caw'. |
| back_elbo | The Evidence lower bound. |
| back_fix | Fixed point iteration for BACKWASH. |
| back_obj | Objective function for BACKWASH. |
| back_update_phi | Update for the "g" hyperparameter. |
| back_update_pi | Update for the prior mixing proportions. |
| back_update_qbeta | Update for the variational density of beta |
| back_update_v | Update for the variational density of v. |
| back_update_xi | Update for the variance scaling parameter. |
| backwash | BACKWASH: Bayesian Adjustment for Confounding Knitted With... |
| backwash_second_step | Second step of the backwash procedure. |
| bfa_gd_gibbs | Fast Gibbs sampler for Bayesian factor analysis. |
| bfa_gs | Bayesian factor analysis used in Gerard and Stephens (2021). |
| bfa_gs_linked | Simple Bayesian low rank matrix decomposition. |
| bfa_gs_linked_gibbs | Fast Gibbs sampler for Bayesian factor analysis. |
| bfa_gs_linked_gibbs_r | R implementation of 'bfa_gs_linked_gibbs'. |
| bfa_wrapper | Wrapper for the bfa package. |
| bfl | Simple Bayesian low rank matrix decomposition. |
| brent_obj_norm | Objective function for updating variance inflation parameter... |
| bsvd | Gibbs sampler for Bayesian SVD. |
| calc_lfsr | Empirical estimate of lfsr based on posterior samples. |
| calc_lfsr_g | Same as 'calc_lfsr' except with a prior specification. |
| calc_mean_g | Calculate moments of pointmass rv's. |
| calc_quantiles_g | Calculate quantiles of pointmass rv's. |
| caw | Iterative procedure for confounder correction with a... |
| clean_my_p | Use the distribution of control genes' p-values to adjust all... |
| clean_my_stats | Quantile normalize stats to their theoretical distributions. |
| cruv4 | RUV4's second step. |
| cruv4_multicov | RUV4's second step. |
| dnormalmix | Density of a mixture of normals |
| dt_wrap | Wrapper for dt with a non-zero mean and non-1 scale... |
| em_miss | EM algorithm for factor analysis with missing block matrix. |
| em_miss_fix | Fixed point iteration for em algorithm with missing block. |
| em_miss_fix_fast | Faster version of 'em_miss_fix'. |
| em_miss_obj | The objective function for em with a missing block. |
| em_miss_obj_fast | A faster version of em_miss_obj. |
| fa_ml | Wrapper for cate's fa.em function. |
| fa_out_test | Test output form fa_func. |
| fa_tester | Tests whether a user-specified factor analysis function is... |
| fa_tester_ruvb | Test whether a user-specified function is compatible with... |
| fix_caw | A fixed point iteration for CAW. |
| fix_caw_wrapper | A wrapper for 'fix_caw' so that I can use SQUAREM. |
| gdfa | Old version of Bayesian factor analysis. |
| get_grid_var | Default way to set grid of variances. |
| hard_impute | My version of hard imputation that begins at the ruv... |
| hier_fun | Hierarchical prior density function as described in Gerard... |
| impute_block | Constructs an overall matrix, then applies a given imputation... |
| impute_ruv_reproduce | Reproduce RUV2, RUV3, and RUV4 with RUVimpute. |
| initialize_mixing_prop | Function for initializing mixing proportions. |
| knn_wrapper | Wrapper for impute.knn |
| missforest_wrapper | Wrapper for missForest package. |
| mouthwash | MOUTHWASH: Maximize Over Unobservables To Help With Adaptive... |
| mouthwash_coordinate | Coordinate ascent for optimizing t likelihood with uniform... |
| mouthwash_second_step | The second step of MOUTHWASH. |
| mouthwash_z_grad | Gradient wrt z of 'uniform_mix_llike'. |
| normal_mix_fix | A fixed point iteration for updating the mixing proportions... |
| normal_mix_fix_wrapper | Wrapper for 'normal_mix_fix' so that I can use SQUAREM. |
| normal_mix_llike | Penalized MOUTHWASH likelihood when using a mixture of... |
| normal_mix_llike_wrapper | Wrapper for 'normal_mix_llike' so that I can use it in... |
| normal_prior | A basic normal prior density function. |
| pca_2step | PCA when first 'vr' rows have a variance multiplicatively... |
| pca_naive | Basic PCA. |
| pca_ruv2 | PCA when first 'vr' rows have a variance multiplicatively... |
| pcaruv2_fix | Fix point for mle in pca_ruv2. |
| pcaruv2_obj | The objective function for mle in pca_ruv2. |
| plot.backwash | Plotting method for 'backwash'. |
| plot.mouthwash | Plotting method for 'moutwash'. |
| plot.ruvb | Plotting method for 'ruvb'. |
| prior_fun_wrapper | Wrapper for 'prior_fun' so that can be called in apply. |
| ptdiff | More stable way to calculate differences in T cdf's. |
| ptdiff_mat | More stable way to calculate differences in T cdfs when input... |
| ptdiff_mat_log | Log version of 'ptdiff_mat'. |
| pt_wrap | Wrapper for pt with a non-zero mena and non-1 scale... |
| qmle_obj | Objective function for quasi-mle approach. |
| qmle_obj_basic | Basic no optimized code objective function. |
| qmle_ruv2 | Quasi-mle when first 'vr' rows of 'Y' have variances which... |
| qmle_ruv2_lambda_grid | Quasi-mle when first 'vr' rows of 'Y' have variances which... |
| qr_ident | An identified QR decomposition. |
| rmixnorm | Draw from a mixture of normals. |
| rnormalmix | Random draw from a mixture of normals. |
| rotate_model | QR rotation to independent models. |
| rubin_copy | Very inefficient copy of Rubin and Thayer iteration mostly... |
| ruv3 | Removing Unwanted Variation 3. |
| ruvb | Bayesian version of Removing Unwanted Variation. |
| ruvem | Same as ruvimpute but only does ruvem and comes up with... |
| ruvimpute | General imputation framework. |
| sim_gtex | A simulated RNA-seq dataset. |
| smell_my_p | Wrapper for a Kolmogorov-Smirnov test using the p-values from... |
| smell_my_stats | Wrapper for a Kolmogorov-Smirnov test using the statistics... |
| softimpute_wrapper | A wrapper for using the softImpute function from the... |
| tregress_em | EM algorithm to find regression coefficients using... |
| tregress_fix | Fixed point iteration for EM algorithm for regression with... |
| tregress_obj | The likelihood for regression with t-errors where the... |
| tregress_obj_wrapper | Wrapper for 'tregress_obj'. |
| unif_int_grad | Gradient wrt z2 of intermediate function in EM. |
| unif_int_obj | Intermediate objective function in EM. |
| uniform_mix_fix | Fixed point iteration when using t errors and a mixture of... |
| uniform_mix_fix_wrapper | Wrapper for 'uniform_mix_fix', mostly so I can use SQUAREM. |
| uniform_mix_llike | Log-likelihood when using t errors and mixture of uniforms... |
| uniform_mix_llike_wrapper | Wrapper for 'uniform_mix_llike', mostly for the SQUAREM... |
| update_f | Utility function for updating F in 'gdfa'. |
| update_lambda | Wrapper for 'optim' and 'qmle_obj'. |
| update_sig_alpha | Fast update for sig_diag and alpha. |
| update_sig_alpha_basic | Basic no optimized code update for sig_diag and alpha. |
| vicar | 'vicar': Various Ideas for Confounder Adjustment in... |
| vruv2 | Calibrated RUV2. |
| vruv2_old | Old version of Calibrated RUV2 that doesn't really work. |
| vruv4 | Calibrated RUV4 where the control genes are used to estimate... |
| vruvinv | Variance inflated RUV-inverse. |
