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 |
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. |
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 |
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' |
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. |
get.filt_feat.matrix | get.filt_feat.matrix |
get.norm_feat.matrix | get.norm_feat.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.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. |
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. |
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 |
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' |
read.label | Read label file |
read.lefse | read an input file in a LEfSe input format |
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 |
train.model | Model training |
validate.data | Validate samples in labels, features, and metadata |
weight_matrix | Retrieve weight_matrix from object. |
weight_matrix-method | Retrieve weight_matrix from object. |