Man pages for biobakery/MMUPHin
Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies
| add_back_covariates | Add back covariate effects to batch-corrected feature... |
| adjust_batch | Zero-inflated empirical Bayes adjustment of batch effect in... |
| adjust_EB | Perform batch adjustment on standardized feature abundances,... |
| aprior | EB prior estimation for scale parameters |
| AST | AST transformation (modified from Maaslin2 and is different) |
| back_transform_abd | Transform batch adjusted feature abundances back to the... |
| bprior | EB prior estimation for scale parameters |
| catchToList | Utility for catching warning/error messages |
| check_batch | Check batch variable |
| check_covariates | Check covariates |
| check_covariates_random | Check random covariates |
| check_D | Check dissimilarity object |
| check_exposure | Check exposure variable |
| check_feature_abd | Check feature abundance table |
| check_metadata | Check that metadata data frame has all the variables and not... |
| check_options | Utility for checking options |
| check_options_continuous | Utility for checking continuous options |
| check_pseudo_count | Utility for checking pseudo count |
| check_rank | Check if a design matrix is full rank |
| check_samples | Check that sample numbers and names match between a feature... |
| check_samples_D | Check that sample numbers and names match between a... |
| construct_design | Construct a design model matrix given a metadata data frame,... |
| construct_ind | Create indicator matrices for which feature/batch/samples to... |
| continuous_discover | Unsupervised meta-analytical discovery and validation of... |
| CRC_abd | Species level feature abundance data of five public CRC... |
| CRC_meta | Sample metadata of five public CRC studies |
| create_table_maaslin | Utility for generating empty Maaslin2 results table |
| diagnostic_adjust_batch | Diagnostic visualization for adj_batch function |
| diagnostic_continuous_discover | Diagnostic visualization for continuous.discover function |
| diagnostic_discrete_discover | Diagnostic visualization for discrete.discover function |
| discrete_discover | Unsupervised meta-analytical discovery and validation of... |
| fill_dimnames | Fill in artificial row/column names to a matrix or data... |
| fit_EB | Parametric estimation of per-batch location and scale... |
| fit_shrink | A posteriori shrink per-batch location and scale parameters... |
| fit_stand_feature | Fit lm and standardize all features |
| it_sol | Iteratively solve for one feature's shrinked location and... |
| lm_meta | Covariate adjusted meta-analytical differential abundance... |
| LOG | LOG transformation (modified from Maaslin2 and is different) |
| Maaslin2_wrapper | Wrapper function for Maaslin2 |
| match_control | Match user-specified control parameters with default, and... |
| normalize_features | Normalize feature abundance table (modified from Maaslin2) |
| relocate_scale | Relocate and scale feature abundances to correct for batch... |
| rename_maaslin | Utility for temporarily renaming samples/features for... |
| rma_wrapper | Wrapper for fitting fixed/random effects meta-analysis model... |
| set_pseudo | Set pseudo count for an abundance matrix. Pseudo count is... |
| shorten_name | Utility for shorter names Useful when plotting per-feature... |
| standardize_feature | Centralize (by design matrix) and standardize (by pooled... |
| transform_features | Transform feature abunadnce table (modified from Maaslin2) |
| tss | TSS normalization (modified from Maaslin2) |
| vaginal_abd | Species level feature abundance data of two public vaginal... |
| vaginal_meta | Sample metadata of two public vaginal studies |
| visualize_continuous_discover | Visualization of the clustered network for the... |
