# Statistical Inference of Associations between Microbial Communities And host phenoTypes

## Documentation for package ‘SIAMCAT’ version 2.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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