All functions

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

data_split<-

Assign a new data_split object to x

eval_data<-

Assign a new eval_data object to x

features<-

Assign a new otu_table object to x features slot

label<-

Assign a new label object to x

meta<-

Assign a new sam_data object to x

model_list<-

Assign a new model_list object to x

norm_param<-

Assign a new norm_param object to x

orig_feat<-

Assign a new otu_table object to x orig_feat slot

physeq<-

Assign a new phyloseq object to x

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-class

The S4 class for storing data splits

data_split

Retrieve a data_split-class object from object.

eval_data-class

The S4 class for storing evaluation data.

eval_data

Retrieve eval_data from object.

evaluate.predictions

Evaluate prediction results

features

Retrieve a otu_table-class object from object.

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-class

The S4 class for storing label info.

label

Retrieve a label-class object from object.

make.predictions

Make predictions on a test set

meta

Retrieve a sample_data-class object from object.

model.evaluation.plot

Model Evaluation Plot

model.interpretation.plot

Model Interpretation Plot

model_list-class

The S4 class for storing models.

model_list models model_type

Retrieve model_list-class from object.

model_type

Retrieve model_type from object.

models

Retrieve list of models from object.

norm_param

Retrieve norm_param from object.

normalize.features

Perform feature normalization

orig_feat

Retrieve a otu_table-class object from orig_feat slot.

physeq

Retrieve a phyloseq-class object from object.

pred_matrix-class

The S4 class for storing label info.

pred_matrix

Retrieve pred_matrix from object.

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-class

The S4 class for storing taxa-abundance information and models.

siamcat

siamcat

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