SIAMCAT-package         SIAMCAT: Statistical Inference of Associations
                        between Microbial Communities And host
                        phenoTypes
accessSlot              Universal slot accessor function for
                        siamcat-class.
add.meta.pred           Add metadata as predictors
assoc_param             Retrieve the list of parameters for association
                        testing from a SIAMCAT object
associations            Retrieve the results of association testing
                        from a SIAMCAT object
associations<-          Assign a new assocications object to 'x'
check.associations      Check and visualize associations between
                        features and classes
check.confounders       Check for potential confounders in the metadata
create.data.split       Split a dataset into training and a test sets.
create.label            Create a label list
data_split              Retrieve the data split from a SIAMCAT object
data_split<-            Assign a new list containing a cross-validation
                        split to a SIAMCAT object
eval_data               Retrieve the evaluation metrics from a SIAMCAT
                        object
eval_data<-             Assign a new list with evaluation data to a
                        SIAMCAT object
evaluate.predictions    Evaluate prediction results
feat.crc.zeller         Example feature matrix
feature_type            Retrieve the feature type used for model
                        training from a SIAMCAT object
feature_weights         Retrieve the matrix of feature weights from a
                        SIAMCAT object
filt_feat               Retrieve the information stored in the
                        'filt_feat' slot within a SIAMCAT object
filt_feat<-             Assign a new filt_feat object to 'x'
filt_params             Retrieve the list of parameters for feature
                        filtering from a SIAMCAT object
filter.features         Perform unsupervised feature filtering.
filter.label            Filter the label of a SIMACAT object
get.filt_feat.matrix    Retrieve the filtered features from a SIAMCAT
                        object
get.norm_feat.matrix    Retrieve the normalized features from a SIAMCAT
                        object
get.orig_feat.matrix    Retrieve the original features from a SIAMCAT
                        object
label                   Retrieve the label from a SIAMCAT object
label<-                 Assign a new label object to a SIAMCAT object
make.predictions        Make predictions on a test set
meta                    Retrieve the metadata from a SIAMCAT object
meta.crc.zeller         Example metadata matrix
meta<-                  Assign a new sam_data object to 'x'
model.evaluation.plot   Model Evaluation Plot
model.interpretation.plot
                        Model Interpretation Plot
model_list              Retrieve the information stored in the
                        'model_list' slot within a SIAMCAT object
model_list<-            Assign a new list containing trained models to
                        a SIAMCAT object
model_type              Retrieve the machine learning method from a
                        SIAMCAT object
models                  Retrieve list of trained models from a SIAMCAT
                        object
norm_feat               Retrieve the information stored in the
                        'norm_feat' slot within a SIAMCAT object
norm_feat<-             Assign a new list containing normalziation
                        parameters and normalized features to a SIAMCAT
                        object
norm_params             Retrieve the list of parameters for feature
                        normalization from a SIAMCAT object
normalize.features      Perform feature normalization
orig_feat               Retrieve a otu_table-class object from
                        otu_table slot in the phyloseq slot in a
                        siamcat object
orig_feat<-             Assign a new otu_table object to 'x' orig_feat
                        slot
physeq                  Retrieve a phyloseq-class object from object.
physeq<-                Assign a new phyloseq object to 'x'
pred_matrix             Retrieve the prediction matrix from a SIAMCAT
                        object
pred_matrix<-           Assign a new matrix with predictions to a
                        SIAMCAT object
read.label              Read label file
read.lefse              read an input file in a LEfSe input format
select.samples          Select samples based on metadata
siamcat                 SIAMCAT constructor function
siamcat-class           The S4 SIAMCAT class
siamcat.to.lefse        create a lefse input file from siamcat object
siamcat_example         SIAMCAT example
train.model             Model training
validate.data           Validate samples in labels, features, and
                        metadata
weight_matrix           Retrieve the weight matrix from a SIAMCAT
                        object
