The SIAMCAT class


The S4 SIAMCAT class stores the results from the SIAMCAT workflow in different slots. The different slots will be filled by different functions (referenced in the description below).

In order to contruct a SIAMCAT class object, please refer to the documentation of the construction function siamcat.

The SIAMCAT class is based on the phyloseq-class. Therefore, you can easily import a phyloseq object into SIAMCAT.



object of class phyloseq-class


list containing the label information for the samples and some metadata about the label, created by create.label or when creating the siamcat-class object by calling siamcat


list containing the filtered features as matrix and the list of filtering parameters, created by calling the filter.features function


list containing the parameters for association testing and the results of association testing with these parameters in a dataframe, created by calling the check.associations function


list containing the normalized features as matrix and the list of normalziation parameters (for frozen normalization), created by calling the normalize.features function


list containing cross-validation instances, created by calling the function


list containing the trained models, the type of model that was trained, and on which kind of features it was trained, created by calling the train.model function


matrix of predictions, created by calling the make.predictions function


list containing different evaluation metrics, created by calling the evaluate.predictions function