SIAMCAT-package | SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes |
accessSlot | Universal slot accessor function for siamcat-class. |
add.meta.pred | Add metadata as predictors |
assign-data_split | Assign a new data_split object to 'x' |
assign-eval_data | Assign a new eval_data object to 'x' |
assign-features | Assign a new otu_table object to 'x' features slot |
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_param | Assign a new norm_param 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' |
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. |
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' |
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' |
features | Retrieve a otu_table-class object from object. |
features-method | Retrieve a otu_table-class object from object. |
features<- | Assign a new otu_table object to 'x' features slot |
features<--method | Assign a new otu_table object to 'x' features slot |
filter.features | Perform unsupervised feature filtering. |
filter.label | Filter samples from 'siamcat@label' |
get.features.matrix | get.features.matrix |
get.orig_feat.matrix | get.orig_feat.matrix |
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' |
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<- | 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. |
normalize.features | Perform feature normalization |
norm_param | Retrieve norm_param from object. |
norm_param-method | Retrieve norm_param from object. |
norm_param<- | Assign a new norm_param object to 'x' |
norm_param<--method | Assign a new norm_param object to 'x' |
orig_feat | Retrieve a otu_table-class object from orig_feat slot. |
orig_feat-class | The S4 class for storing original features info. |
orig_feat-method | Retrieve a label-class object from object. |
orig_feat-method | Retrieve a otu_table-class object from orig_feat slot. |
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 |
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 label info. |
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' |
read.features | Read feature file |
read.labels | Read labels file |
read.meta | Read metadata file |
reset.features | reset.features |
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_example | Documentation for the example siamcat object in the data folder |
train.model | Model training |
validate.data | Validate samples in labels, features, and metadata |