| SIAMCAT-package | SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes |
| add.meta.pred | Add metadata as predictors |
| association.plot | Visualize associations between features and classes |
| associations | Retrieve the results of association testing from a SIAMCAT object |
| associations-method | Retrieve the results of association testing from a SIAMCAT object |
| assoc_param | Retrieve the list of parameters for association testing from a SIAMCAT object |
| assoc_param-method | Retrieve the list of parameters for association testing from a SIAMCAT object |
| assoc_param_param | Retrieve the list of parameters for association testing from a SIAMCAT object |
| check.associations | Calculate associations between features and labels |
| 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-method | Retrieve the data split from a SIAMCAT object |
| evaluate.predictions | Evaluate prediction results |
| eval_data | Retrieve the evaluation metrics from a SIAMCAT object |
| eval_data-method | Retrieve the evaluation metrics from a SIAMCAT object |
| feat.crc.zeller | Example feature matrix |
| feature_type | Retrieve the feature type used for model training from a SIAMCAT object |
| feature_type-method | Retrieve the feature type used for model training from a SIAMCAT object |
| feature_weights | Retrieve the matrix of feature weights from a SIAMCAT object |
| feature_weights-method | Retrieve the matrix of feature weights from a SIAMCAT object |
| filter.features | Perform unsupervised feature filtering. |
| filter.label | Filter the label of a SIMACAT object |
| filt_params | Retrieve the list of parameters for feature filtering from a SIAMCAT object |
| filt_params-method | Retrieve the list of parameters for feature filtering from a SIAMCAT 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-method | Retrieve the label from a SIAMCAT object |
| make.predictions | Make predictions on a test set |
| meta | Retrieve the metadata from a SIAMCAT object |
| meta-method | Retrieve the metadata from a SIAMCAT object |
| meta.crc.zeller | Example metadata matrix |
| model.evaluation.plot | Model Evaluation Plot |
| model.interpretation.plot | Model Interpretation Plot |
| models | Retrieve list of trained models from a SIAMCAT object |
| models-method | Retrieve list of trained models from a SIAMCAT object |
| model_type | Retrieve the machine learning method from a SIAMCAT object |
| model_type-method | Retrieve the machine learning method from a SIAMCAT object |
| normalize.features | Perform feature normalization |
| norm_params | Retrieve the list of parameters for feature normalization from a SIAMCAT object |
| norm_params-method | Retrieve the list of parameters for feature normalization from a SIAMCAT object |
| pred_matrix | Retrieve the prediction matrix from a SIAMCAT object |
| pred_matrix-method | Retrieve the prediction matrix from a SIAMCAT object |
| read.label | Read label file |
| select.samples | Select samples based on metadata |
| SIAMCAT | SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes |
| siamcat | SIAMCAT constructor function |
| siamcat-class | The S4 SIAMCAT class |
| siamcat_example | SIAMCAT example |
| train.model | Model training |
| validate.data | Validate samples in labels, features, and metadata |
| volcano.plot | Visualize associations between features and classes as volcano plot |
| weight_matrix | Retrieve the weight matrix from a SIAMCAT object |
| weight_matrix-method | Retrieve the weight matrix from a SIAMCAT object |