Man pages for KonradZych/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-data_split | Assign a new data_split object to 'x' |
| assign-eval_data | Assign a new eval_data object to 'x' |
| assign-features | Assign a new otu_table object to 'x' features slot |
| assign-label | Assign a new label object to 'x' |
| assign-meta | Assign a new sam_data object to 'x' |
| assign-model_list | Assign a new model_list object to 'x' |
| assign-norm_param | Assign a new norm_param object to 'x' |
| 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 pred_matrix 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.from.metadata | create a label object from metadata |
| data_split-class | The S4 class for storing data splits |
| data_split-methods | Retrieve a data_split-class object from object. |
| eval_data-class | The S4 class for storing evaluation data. |
| eval_data-methods | Retrieve eval_data from object. |
| evaluate.predictions | Evaluate prediction results |
| features-methods | Retrieve a otu_table-class object from object. |
| filter.features | Perform unsupervised feature filtering. |
| filter.label | Filter samples from 'siamcat@label' |
| get.component.classes | Show the component objects classes and slot names. |
| get.features.matrix | get.features.matrix |
| get.orig_feat.matrix | get.orig_feat.matrix |
| label-class | The S4 class for storing label info. |
| label-methods | Retrieve a label-class object from object. |
| make.predictions | Make predictions on a test set |
| meta-methods | Retrieve a sample_data-class object from object. |
| model.evaluation.plot | Model Evaluation Plot |
| model.interpretation.plot | Model Interpretation Plot |
| model_list-class | The S4 class for storing models. |
| model_list-methods | Retrieve model_list-class from object. |
| models-methods | Retrieve list of models from object. |
| model_type-methods | Retrieve model_type from object. |
| normalize.features | Perform feature normalization |
| norm_param-class | The S4 class for storing the normalization paramters |
| norm_param-methods | Retrieve norm_param from object. |
| orig_feat-class | The S4 class for storing original features info. |
| orig_feat-methods | Retrieve a otu_table-class object from orig_feat slot. |
| parse.label.header | Parse label header |
| physeq-methods | Retrieve a phyloseq-class object from object. |
| pred_matrix-class | The S4 class for storing label info. |
| pred_matrix-methods | Retrieve pred_matrix from object. |
| read.features | Read feature file |
| read.labels | Read labels file |
| read.lefse | read an input file in a LEfSe input format |
| read.meta | Read metadata file |
| reset.features | reset.features |
| select.samples | Select samples based on metadata |
| show-methods | Show method for siamcat class object |
| siamcat | siamcat |
| siamcat-class | The S4 class for storing taxa-abundance information and... |
| siamcat_example | Documentation for the example siamcat object in the data... |
| 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 |
| train.model | Model training |
| validate.data | Validate samples in labels, features, and metadata |
