Man pages for 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... |
| 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... |
| assign-norm_feat | Assign a new list containing normalziation parameters and... |
| 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-methods | Retrieve the results of association testing from a SIAMCAT... |
| assoc_param-methods | Retrieve the list of parameters for association testing from... |
| 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-methods | Retrieve the data split from a SIAMCAT object |
| eval_data-methods | Retrieve the evaluation metrics from a SIAMCAT object |
| evaluate.predictions | Evaluate prediction results |
| feat.crc.zeller | Example feature matrix |
| feature_type-methods | Retrieve the feature type used for model training from a... |
| feature_weights-methods | 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-methods | Retrieve the information stored in the 'filt_feat' slot... |
| filt_params-methods | Retrieve the list of parameters for feature filtering from a... |
| get.component.classes | Show the component objects classes and slot names. |
| 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-methods | Retrieve the label from a SIAMCAT object |
| make.predictions | Make predictions on a test set |
| meta.crc.zeller | Example metadata matrix |
| meta-methods | Retrieve the metadata from a SIAMCAT object |
| model.evaluation.plot | Model Evaluation Plot |
| model.interpretation.plot | Model Interpretation Plot |
| model_list-methods | Retrieve the information stored in the 'model_list' slot... |
| models-methods | Retrieve list of trained models from a SIAMCAT object |
| model_type-methods | Retrieve the machine learning method from a SIAMCAT object |
| normalize.features | Perform feature normalization |
| norm_feat-methods | Retrieve the information stored in the 'norm_feat' slot... |
| norm_params-methods | Retrieve the list of parameters for feature normalization... |
| orig_feat-methods | Retrieve a otu_table-class object from otu_table slot in the... |
| parse.label.header | Parse label header |
| physeq-methods | Retrieve a phyloseq-class object from object. |
| pred_matrix-methods | Retrieve the prediction matrix from 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 |
| show-methods | Show method for siamcat class object |
| siamcat | SIAMCAT constructor function |
| siamcat-class | The S4 SIAMCAT class |
| siamcat_example | SIAMCAT example |
| SIAMCAT-package | SIAMCAT: Statistical Inference of Associations between... |
| siamcat.to.lefse | create a lefse input file from siamcat object |
| siamcat.to.maaslin | create a MaAsLin input file from siamcat object |
| summarize.features | Summarize features |
| train.model | Model training |
| validate.data | Validate samples in labels, features, and metadata |
| weight_matrix-methods | Retrieve the weight matrix from a SIAMCAT object |
