Man pages for KonradZych/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-data_splitAssign a new data_split object to 'x'
assign-eval_dataAssign a new eval_data object to 'x'
assign-featuresAssign a new otu_table object to 'x' features slot
assign-labelAssign a new label object to 'x'
assign-metaAssign a new sam_data object to 'x'
assign-model_listAssign a new model_list object to 'x'
assign-norm_paramAssign a new norm_param object to 'x'
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 pred_matrix object to 'x'
check.associationsCheck and visualize associations between features and classes
check.confoundersCheck for potential confounders in the metadata
create.data.splitSplit a dataset into training and a test sets.
create.label.from.metadatacreate a label object from metadata
data_split-classThe S4 class for storing data splits
data_split-methodsRetrieve a data_split-class object from object.
eval_data-classThe S4 class for storing evaluation data.
eval_data-methodsRetrieve eval_data from object.
evaluate.predictionsEvaluate prediction results
features-methodsRetrieve a otu_table-class object from object.
filter.featuresPerform unsupervised feature filtering.
filter.labelFilter samples from '[email protected]'
get.component.classesShow the component objects classes and slot names.
get.features.matrixget.features.matrix
get.orig_feat.matrixget.orig_feat.matrix
label-classThe S4 class for storing label info.
label-methodsRetrieve a label-class object from object.
make.predictionsMake predictions on a test set
meta-methodsRetrieve a sample_data-class object from object.
model.evaluation.plotModel Evaluation Plot
model.interpretation.plotModel Interpretation Plot
model_list-classThe S4 class for storing models.
model_list-methodsRetrieve model_list-class from object.
models-methodsRetrieve list of models from object.
model_type-methodsRetrieve model_type from object.
normalize.featuresPerform feature normalization
norm_param-classThe S4 class for storing the normalization paramters
norm_param-methodsRetrieve norm_param from object.
orig_feat-classThe S4 class for storing original features info.
orig_feat-methodsRetrieve a otu_table-class object from orig_feat slot.
parse.label.headerParse label header
physeq-methodsRetrieve a phyloseq-class object from object.
pred_matrix-classThe S4 class for storing label info.
pred_matrix-methodsRetrieve pred_matrix from object.
read.featuresRead feature file
read.labelsRead labels file
read.lefseread an input file in a LEfSe input format
read.metaRead metadata file
reset.featuresreset.features
select.samplesSelect samples based on metadata
show-methodsShow method for siamcat class object
siamcatsiamcat
siamcat-classThe S4 class for storing taxa-abundance information and...
siamcat_exampleDocumentation for the example siamcat object in the data...
SIAMCAT-packageSIAMCAT: Statistical Inference of Associations between...
siamcat.to.lefsecreate a lefse input file from siamcat object
siamcat.to.maaslincreate a MaAsLin input file from siamcat object
train.modelModel training
validate.dataValidate samples in labels, features, and metadata
KonradZych/SIAMCAT documentation built on June 6, 2018, 5:30 a.m.