# Statistical Inference of Associations between Microbial Communities And host phenoTypes

## Documentation for package ‘SIAMCAT’ version 2.0.1

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

## Help Pages

A C D E F G L M N O P R S T V W

SIAMCAT-package | SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes

## -- A --

accessSlot | Universal slot accessor function for siamcat-class.
add.meta.pred | Add metadata as predictors
assign-associations | Assign a new assocications object to 'x'
assign-data_split | Assign a new list containing a cross-validation split to a SIAMCAT object
assign-eval_data | Assign a new list with evaluation data to a SIAMCAT object
assign-filt_feat | Assign a new filt_feat object to 'x'
assign-label | Assign a new label object to a SIAMCAT object
assign-meta | Assign a new sam_data object to 'x'
assign-model_list | Assign a new list containing trained models to a SIAMCAT object
assign-norm_feat | Assign a new list containing normalziation parameters and normalized features to a SIAMCAT object
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 matrix with predictions to a SIAMCAT object
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
associations<- | Assign a new assocications object to 'x'
associations<--method | Assign a new assocications object to 'x'
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

## -- C --

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 | Create a label list

## -- D --

data_split | Retrieve the data split from a SIAMCAT object
data_split-method | Retrieve the data split from a SIAMCAT object
data_split<- | Assign a new list containing a cross-validation split to a SIAMCAT object
data_split<--method | Assign a new list containing a cross-validation split to a SIAMCAT object

## -- E --

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
eval_data<- | Assign a new list with evaluation data to a SIAMCAT object
eval_data<--method | Assign a new list with evaluation data to a SIAMCAT object

## -- F --

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_feat | Retrieve the information stored in the 'filt_feat' slot within a SIAMCAT object
filt_feat-method | Retrieve the information stored in the 'filt_feat' slot within a SIAMCAT object
filt_feat<- | Assign a new filt_feat object to 'x'
filt_feat<--method | Assign a new filt_feat object to 'x'
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

## -- G --

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

## -- L --

label | Retrieve the label from a SIAMCAT object
label-method | Retrieve the label from a SIAMCAT object
label<- | Assign a new label object to a SIAMCAT object
label<--method | Assign a new label object to a SIAMCAT object
LearnerClassifLiblineaR | LiblineaR Classification Learner

## -- M --

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
meta<- | Assign a new sam_data object to 'x'
meta<--method | Assign a new sam_data object to 'x'
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_list | Retrieve the information stored in the 'model_list' slot within a SIAMCAT object
model_list-method | Retrieve the information stored in the 'model_list' slot within a SIAMCAT object
model_list<- | Assign a new list containing trained models to a SIAMCAT object
model_list<--method | Assign a new list containing trained models to 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

## -- N --

normalize.features | Perform feature normalization
norm_feat | Retrieve the information stored in the 'norm_feat' slot within a SIAMCAT object
norm_feat-method | Retrieve the information stored in the 'norm_feat' slot within a SIAMCAT object
norm_feat<- | Assign a new list containing normalziation parameters and normalized features to a SIAMCAT object
norm_feat<--method | Assign a new list containing normalziation parameters and normalized features to a SIAMCAT object
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

## -- O --

orig_feat | Retrieve a otu_table-class object from otu_table slot in the phyloseq slot in a siamcat object
orig_feat-method | Retrieve a otu_table-class object from otu_table slot in the phyloseq slot in a siamcat object
orig_feat<- | Assign a new otu_table object to 'x' orig_feat slot
orig_feat<--method | Assign a new otu_table object to 'x' orig_feat slot

## -- P --

physeq | Retrieve a phyloseq-class object from object.
physeq-method | Retrieve a phyloseq-class object from object.
physeq<- | Assign a new phyloseq object to 'x'
physeq<--method | Assign a new phyloseq object to 'x'
pred_matrix | Retrieve the prediction matrix from a SIAMCAT object
pred_matrix-method | Retrieve the prediction matrix from a SIAMCAT object
pred_matrix<- | Assign a new matrix with predictions to a SIAMCAT object
pred_matrix<--method | Assign a new matrix with predictions to a SIAMCAT object

## -- R --

read.label | Read label file
read.lefse | read an input file in a LEfSe input format

## -- S --

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.to.lefse | create a LEfSe input file from SIAMCAT object
siamcat_example | SIAMCAT example

## -- T --

train.model | Model training

## -- V --

validate.data | Validate samples in labels, features, and metadata
volcano.plot | Visualize associations between features and classes as volcano plot

## -- W --

weight_matrix | Retrieve the weight matrix from a SIAMCAT object
weight_matrix-method | Retrieve the weight matrix from a SIAMCAT object