Man pages for zellerlab/siamcat
Statistical Inference of Associations between Microbial Communities And host phenoTypes

accessSlotUniversal slot accessor function for siamcat-class.
add.meta.predAdd metadata as predictors
assign-associationsAssign a new assocications object to 'x'
assign-data_splitAssign a new list containing a cross-validation split to a...
assign-eval_dataAssign a new list with evaluation data to a SIAMCAT object
assign-filt_featAssign a new filt_feat object to 'x'
assign-labelAssign a new label object to a SIAMCAT object
assign-metaAssign a new sam_data object to 'x'
assign-model_listAssign a new list containing trained models to a SIAMCAT...
assign-norm_featAssign a new list containing normalziation parameters and...
assign-orig_featAssign a new otu_table object to 'x' orig_feat slot
assign-physeqAssign a new phyloseq object to 'x'
assign-pred_matrixAssign a new matrix with predictions to a SIAMCAT object
associations-methodsRetrieve the results of association testing from a SIAMCAT...
assoc_param-methodsRetrieve the list of parameters for association testing from...
check.associationsCheck and visualize associations between features and classes
check.confoundersCheck for potential confounders in the metadata a dataset into training and a test sets.
create.labelCreate a label list
data_split-methodsRetrieve the data split from a SIAMCAT object
eval_data-methodsRetrieve the evaluation metrics from a SIAMCAT object
evaluate.predictionsEvaluate prediction results
feat.crc.zellerExample feature matrix
feature_type-methodsRetrieve the feature type used for model training from a...
feature_weights-methodsRetrieve the matrix of feature weights from a SIAMCAT object
filter.featuresPerform unsupervised feature filtering.
filter.labelFilter the label of a SIMACAT object
filt_feat-methodsRetrieve the information stored in the 'filt_feat' slot...
filt_params-methodsRetrieve the list of parameters for feature filtering from a...
get.component.classesShow the component objects classes and slot names.
get.filt_feat.matrixRetrieve the filtered features from a SIAMCAT object
get.norm_feat.matrixRetrieve the normalized features from a SIAMCAT object
get.orig_feat.matrixRetrieve the original features from a SIAMCAT object
label-methodsRetrieve the label from a SIAMCAT object
make.predictionsMake predictions on a test set
meta.crc.zellerExample metadata matrix
meta-methodsRetrieve the metadata from a SIAMCAT object
model.evaluation.plotModel Evaluation Plot
model.interpretation.plotModel Interpretation Plot
model_list-methodsRetrieve the information stored in the 'model_list' slot...
models-methodsRetrieve list of trained models from a SIAMCAT object
model_type-methodsRetrieve the machine learning method from a SIAMCAT object
normalize.featuresPerform feature normalization
norm_feat-methodsRetrieve the information stored in the 'norm_feat' slot...
norm_params-methodsRetrieve the list of parameters for feature normalization...
orig_feat-methodsRetrieve a otu_table-class object from otu_table slot in the...
parse.label.headerParse label header
physeq-methodsRetrieve a phyloseq-class object from object.
pred_matrix-methodsRetrieve the prediction matrix from a SIAMCAT object
read.labelRead label file
read.lefseread an input file in a LEfSe input format
select.samplesSelect samples based on metadata
show-methodsShow method for siamcat class object
siamcatSIAMCAT constructor function
siamcat-classThe S4 SIAMCAT class
siamcat_exampleSIAMCAT example
SIAMCAT-packageSIAMCAT: Statistical Inference of Associations between... a lefse input file from siamcat object a MaAsLin input file from siamcat object
summarize.featuresSummarize features
train.modelModel training
validate.dataValidate samples in labels, features, and metadata
weight_matrix-methodsRetrieve the weight matrix from a SIAMCAT object
zellerlab/siamcat documentation built on Nov. 13, 2020, 8:16 a.m.