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 parameters of association testing from
                        object.
associations            Retrieve associations from object.
associations-class      The S4 class for storing the results of the
                        association testing
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 object from metadata or an
                        atomic vector
data_split              Retrieve a data_split-class object from object.
data_split-class        The S4 class for storing data splits
data_split<-            Assign a new data_split object to 'x'
eval_data               Retrieve eval_data from object.
eval_data-class         The S4 class for storing evaluation data.
eval_data<-             Assign a new eval_data object to 'x'
evaluate.predictions    Evaluate prediction results
feat.crc.zeller         Documentation for the example feature object in
                        the data folder
feature_type            Retrieve feature_type from object.
feature_weights         Retrieve feature_weights from object.
filt_feat               Retrieve filtered features form object
filt_feat-class         The S4 class for storing the filter
                        features/paramters
filt_feat<-             Assign a new filt_feat object to 'x'
filt_params             Retrieve the list of filtering parameters from
                        object.
filter.features         Perform unsupervised feature filtering.
filter.label            Filter samples from 'siamcat@label'
get.filt_feat.matrix    get.filt_feat.matrix
get.norm_feat.matrix    get.norm_feat.matrix
get.orig_feat.matrix    get.orig_feat.matrix
label                   Retrieve a label-class object from object.
label-class             The S4 class for storing label info.
label<-                 Assign a new label object to 'x'
make.predictions        Make predictions on a test set
meta                    Retrieve a sample_data-class object from
                        object.
meta.crc.zeller         Documentation for the example metadata object
                        in the data folder
meta<-                  Assign a new sam_data object to 'x'
model.evaluation.plot   Model Evaluation Plot
model.interpretation.plot
                        Model Interpretation Plot
model_list              Retrieve model_list-class from object.
model_list-class        The S4 class for storing models.
model_list<-            Assign a new model_list object to 'x'
model_type              Retrieve model_type from object.
models                  Retrieve list of models from object.
norm_feat               Retrieve normalized features form object
norm_feat-class         The S4 class for storing the normalization
                        data/parameters
norm_feat<-             Assign a new norm_feat object to 'x'
norm_params             Retrieve the list of normalization parameters
                        from 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 pred_matrix from object.
pred_matrix-class       The S4 class for storing predictions.
pred_matrix<-           Assign a new pred_matrix object to 'x'
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
siamcat-class           The S4 class for storing taxa-abundance
                        information and models.
siamcat.to.lefse        create a lefse input file from siamcat object
siamcat_example         Documentation for the example siamcat object in
                        the data folder
train.model             Model training
validate.data           Validate samples in labels, features, and
                        metadata
weight_matrix           Retrieve weight_matrix from object.
