Man pages for MMUPHin
Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

add_back_covariatesAdd back covariate effects to batch-corrected feature...
adjust_batchZero-inflated empirical Bayes adjustment of batch effect in...
adjust_EBPerform batch adjustment on standardized feature abundances,...
apriorEB prior estimation for scale parameters
ASTAST transformation (modified from Maaslin2 and is different)
back_transform_abdTransform batch adjusted feature abundances back to the...
bpriorEB prior estimation for scale parameters
catchToListUtility for catching warning/error messages
check_batchCheck batch variable
check_covariatesCheck covariates
check_covariates_randomCheck random covariates
check_DCheck dissimilarity object
check_exposureCheck exposure variable
check_feature_abdCheck feature abundance table
check_metadataCheck that metadata data frame has all the variables and not...
check_optionsUtility for checking options
check_options_continuousUtility for checking continuous options
check_pseudo_countUtility for checking pseudo count
check_rankCheck if a design matrix is full rank
check_samplesCheck that sample numbers and names match between a feature...
check_samples_DCheck that sample numbers and names match between a...
construct_designConstruct a design model matrix given a metadata data frame,...
construct_indCreate indicator matrices for which feature/batch/samples to...
continuous_discoverUnsupervised meta-analytical discovery and validation of...
CRC_abdSpecies level feature abundance data of five public CRC...
CRC_metaSample metadata of five public CRC studies
create_table_maaslinUtility for generating empty Maaslin2 results table
diagnostic_adjust_batchDiagnostic visualization for adj_batch function
diagnostic_continuous_discoverDiagnostic visualization for continuous.discover function
diagnostic_discrete_discoverDiagnostic visualization for discrete.discover function
discrete_discoverUnsupervised meta-analytical discovery and validation of...
fill_dimnamesFill in artificial row/column names to a matrix or data...
fit_EBParametric estimation of per-batch location and scale...
fit_shrinkA posteriori shrink per-batch location and scale parameters...
fit_stand_featureFit lm and standardize all features
it_solIteratively solve for one feature's shrinked location and...
lm_metaCovariate adjusted meta-analytical differential abundance...
LOGLOG transformation (modified from Maaslin2 and is different)
Maaslin2_wrapperWrapper function for Maaslin2
match_controlMatch user-specified control parameters with default, and...
normalize_featuresNormalize feature abundance table (modified from Maaslin2)
relocate_scaleRelocate and scale feature abundances to correct for batch...
rename_maaslinUtility for temporarily renaming samples/features for...
rma_wrapperWrapper for fitting fixed/random effects meta-analysis model...
set_pseudoSet pseudo count for an abundance matrix. Pseudo count is...
shorten_nameUtility for shorter names Useful when plotting per-feature...
standardize_featureCentralize (by design matrix) and standardize (by pooled...
transform_featuresTransform feature abunadnce table (modified from Maaslin2)
tssTSS normalization (modified from Maaslin2)
vaginal_abdSpecies level feature abundance data of two public vaginal...
vaginal_metaSample metadata of two public vaginal studies
visualize_continuous_discoverVisualization of the clustered network for the...
MMUPHin documentation built on Oct. 31, 2019, 5:07 a.m.