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A C D E F G L M N O P R S T V W
| 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 |
| assign-associations | Assign a new assocications object to 'x' |
| assign-data_split | Assign a new list containing a cross-validation split to a SIAMCAT object |
| assign-eval_data | Assign a new list with evaluation data to a SIAMCAT object |
| assign-filt_feat | Assign a new filt_feat object to 'x' |
| assign-label | Assign a new label object to a SIAMCAT object |
| assign-meta | Assign a new sam_data object to 'x' |
| assign-model_list | Assign a new list containing trained models to a SIAMCAT object |
| assign-norm_feat | Assign a new list containing normalziation parameters and normalized features to a SIAMCAT object |
| assign-orig_feat | Assign a new otu_table object to 'x' orig_feat slot |
| assign-physeq | Assign a new phyloseq object to 'x' |
| assign-pred_matrix | Assign a new matrix with predictions to a SIAMCAT object |
| associations | Retrieve the results of association testing from a SIAMCAT object |
| associations-method | Retrieve the results of association testing from a SIAMCAT object |
| associations<- | Assign a new assocications object to 'x' |
| associations<--method | Assign a new assocications object to 'x' |
| 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 | 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-method | Retrieve the data split from a SIAMCAT object |
| data_split<- | Assign a new list containing a cross-validation split to a SIAMCAT object |
| data_split<--method | Assign a new list containing a cross-validation split to 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 |
| eval_data<- | Assign a new list with evaluation data to a SIAMCAT object |
| eval_data<--method | Assign a new list with evaluation data to 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_feat | Retrieve the information stored in the 'filt_feat' slot within a SIAMCAT object |
| filt_feat-method | Retrieve the information stored in the 'filt_feat' slot within a SIAMCAT object |
| filt_feat<- | Assign a new filt_feat object to 'x' |
| filt_feat<--method | Assign a new filt_feat object to 'x' |
| 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 |
| label<- | Assign a new label object to a SIAMCAT object |
| label<--method | 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-method | Retrieve the metadata from a SIAMCAT object |
| meta.crc.zeller | Example metadata matrix |
| meta<- | Assign a new sam_data object to 'x' |
| meta<--method | Assign a new sam_data object to 'x' |
| 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_list | Retrieve the information stored in the 'model_list' slot within a SIAMCAT object |
| model_list-method | 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_list<--method | Assign a new list containing trained models to 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_feat | Retrieve the information stored in the 'norm_feat' slot within a SIAMCAT object |
| norm_feat-method | 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_feat<--method | 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 |
| norm_params-method | Retrieve the list of parameters for feature normalization from a SIAMCAT object |
| orig_feat | Retrieve a otu_table-class object from otu_table slot in the phyloseq slot in a siamcat object |
| orig_feat-method | 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 |
| orig_feat<--method | Assign a new otu_table object to 'x' orig_feat slot |
| physeq | Retrieve a phyloseq-class object from object. |
| physeq-method | Retrieve a phyloseq-class object from object. |
| physeq<- | Assign a new phyloseq object to 'x' |
| physeq<--method | Assign a new phyloseq object to 'x' |
| pred_matrix | Retrieve the prediction matrix from a SIAMCAT object |
| pred_matrix-method | Retrieve the prediction matrix from a SIAMCAT object |
| pred_matrix<- | Assign a new matrix with predictions to a SIAMCAT object |
| pred_matrix<--method | 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: Statistical Inference of Associations between Microbial Communities And host phenoTypes |
| 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 |
| weight_matrix-method | Retrieve the weight matrix from a SIAMCAT object |