Statistical Inference of Associations between Microbial Communities And host phenoTypes

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Documentation for package ‘SIAMCAT’ version 1.2.1

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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.