# Statistical Inference of Associations between Microbial Communities And host phenoTypes

## Documentation for package ‘SIAMCAT’ version 1.2.1

- 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 data_split object to 'x'
assign-eval_data | Assign a new eval_data object to 'x'
assign-filt_feat | Assign a new filt_feat object to 'x'
assign-label | Assign a new label object to 'x'
assign-meta | Assign a new sam_data object to 'x'
assign-model_list | Assign a new model_list object to 'x'
assign-norm_feat | Assign a new norm_feat object to 'x'
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 pred_matrix object to 'x'
associations | Retrieve associations from object.
associations-class | The S4 class for storing the results of the association testing
associations-method | Retrieve associations from object.
associations<- | Assign a new assocications object to 'x'
associations<--method | Assign a new assocications object to 'x'
assoc_param | Retrieve parameters of association testing from object.
assoc_param-method | Retrieve parameters of association testing from object.
assoc_param_param-method | Retrieve parameters of association testing from 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 object from metadata or an atomic vector

## -- D --

data_split | Retrieve a data_split-class object from object.
data_split-class | The S4 class for storing data splits
data_split-method | Retrieve a data_split-class object from object.
data_split<- | Assign a new data_split object to 'x'
data_split<--method | Assign a new data_split object to 'x'

## -- E --

evaluate.predictions | Evaluate prediction results
eval_data | Retrieve eval_data from object.
eval_data-class | The S4 class for storing evaluation data.
eval_data-method | Retrieve eval_data from object.
eval_data<- | Assign a new eval_data object to 'x'
eval_data<--method | Assign a new eval_data object to 'x'

## -- F --

feat.crc.zeller | Documentation for the example feature object in the data folder
feature_type | Retrieve feature_type from object.
feature_type-method | Retrieve feature_type from object.
feature_type-method | Retrieve model_list-class from object.
feature_weights | Retrieve feature_weights from object.
feature_weights-method | Retrieve feature_weights from object.
filter.features | Perform unsupervised feature filtering.
filter.label | Filter samples from 'siamcat@label'
filt_feat | Retrieve filtered features form object
filt_feat-class | The S4 class for storing the filter features/paramters
filt_feat-method | Retrieve filtered features form 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 filtering parameters from object.
filt_params-method | Retrieve the list of filtering parameters from object.

## -- G --

get.filt_feat.matrix | get.filt_feat.matrix
get.norm_feat.matrix | get.norm_feat.matrix
get.orig_feat.matrix | get.orig_feat.matrix

## -- L --

label | Retrieve a label-class object from object.
label-class | The S4 class for storing label info.
label-method | Retrieve a label-class object from object.
label<- | Assign a new label object to 'x'
label<--method | Assign a new label object to 'x'

## -- M --

make.predictions | Make predictions on a test set
meta | Retrieve a sample_data-class object from object.
meta-method | Retrieve a sample_data-class object from object.
meta.crc.zeller | Documentation for the example metadata object in the data folder
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 models from object.
models-method | Retrieve model_list-class from object.
models-method | Retrieve list of models from object.
model_list | Retrieve model_list-class from object.
model_list-class | The S4 class for storing models.
model_list-method | Retrieve model_list-class from object.
model_list<- | Assign a new model_list object to 'x'
model_list<--method | Assign a new model_list object to 'x'
model_type | Retrieve model_type from object.
model_type-method | Retrieve model_list-class from object.
model_type-method | Retrieve model_type from object.

## -- N --

normalize.features | Perform feature normalization
norm_feat | Retrieve normalized features form object
norm_feat-class | The S4 class for storing the normalization data/parameters
norm_feat-method | Retrieve normalized features form object
norm_feat<- | Assign a new norm_feat object to 'x'
norm_feat<--method | Assign a new norm_feat object to 'x'
norm_params | Retrieve the list of normalization parameters from object.
norm_params-method | Retrieve the list of normalization parameters from 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 pred_matrix from object.
pred_matrix-class | The S4 class for storing predictions.
pred_matrix-method | Retrieve pred_matrix from object.
pred_matrix<- | Assign a new pred_matrix object to 'x'
pred_matrix<--method | Assign a new pred_matrix object to 'x'

## -- 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
siamcat-class | The S4 class for storing taxa-abundance information and models.
siamcat.to.lefse | create a lefse input file from siamcat object
siamcat_example | Documentation for the example siamcat object in the data folder

## -- T --

train.model | Model training

## -- V --

validate.data | Validate samples in labels, features, and metadata

## -- W --

weight_matrix | Retrieve weight_matrix from object.
weight_matrix-method | Retrieve weight_matrix from object.