All functions |
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SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes |
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Universal slot accessor function for siamcat-class. |
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Add metadata as predictors |
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Assign a new data_split object to |
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Assign a new eval_data object to |
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Assign a new otu_table object to |
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Assign a new label object to |
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Assign a new sam_data object to |
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Assign a new model_list object to |
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Assign a new norm_param object to |
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Assign a new otu_table object to |
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Assign a new phyloseq object to |
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Assign a new pred_matrix object to |
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Check and visualize associations between features and classes |
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Check for potential confounders in the metadata |
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Split a dataset into training and a test sets. |
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The S4 class for storing data splits |
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Retrieve a data_split-class object from object. |
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The S4 class for storing evaluation data. |
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Retrieve eval_data from object. |
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Evaluate prediction results |
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Retrieve a otu_table-class object from object. |
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Perform unsupervised feature filtering. |
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Filter samples from |
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get.features.matrix |
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get.orig_feat.matrix |
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The S4 class for storing label info. |
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Retrieve a label-class object from object. |
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Make predictions on a test set |
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Retrieve a sample_data-class object from object. |
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Model Evaluation Plot |
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Model Interpretation Plot |
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The S4 class for storing models. |
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Retrieve model_list-class from object. |
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Retrieve model_type from object. |
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Retrieve list of models from object. |
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Retrieve norm_param from object. |
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Perform feature normalization |
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Retrieve a otu_table-class object from orig_feat slot. |
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Retrieve a phyloseq-class object from object. |
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The S4 class for storing label info. |
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Retrieve pred_matrix from object. |
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Read feature file |
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Read labels file |
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Read metadata file |
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reset.features |
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Select samples based on metadata |
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The S4 class for storing taxa-abundance information and models. |
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siamcat |
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Documentation for the example siamcat object in the data folder |
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Model training |
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Validate samples in labels, features, and metadata |