Statistical Inference of Associations between Microbial Communities And host phenoTypes

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Documentation for package ‘SIAMCAT’ version 2.9.0

• 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