SIAMCAT-package | SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes |
add.meta.pred | Add metadata as predictors |
association.plot | Visualize associations between features and classes |
associations | Retrieve the results of association testing from a SIAMCAT object |
associations-method | Retrieve the results of association testing from a SIAMCAT object |
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 | Calculate associations between features and labels |
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 |
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 |
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_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 |
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 |
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_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_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 |
pred_matrix | Retrieve the prediction matrix from a SIAMCAT object |
pred_matrix-method | Retrieve the prediction matrix from a SIAMCAT object |
read.label | Read label file |
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_example | SIAMCAT example |
train.model | Model training |
validate.data | Validate samples in labels, features, and metadata |
volcano.plot | Visualize associations between features and classes as volcano plot |
weight_matrix | Retrieve the weight matrix from a SIAMCAT object |
weight_matrix-method | Retrieve the weight matrix from a SIAMCAT object |