Statistical Inference of Associations between Microbial Communities And host phenoTypes


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Documentation for package ‘SIAMCAT’ version 2.12.0

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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