# An R package for colorectal cancer screening and microbiome analysis

## Documentation for package ‘CrcBiomeScreen’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

checkClassBalance | Check the sample distribution of the dataset and give the suggestion if need the class weight or not
CrcBiomeScreen-class | CrcBiomeScreen Class
CreateCrcBiomeScreenObject | Create a CrcBiomeScreen S4 object for microbiome-based CRC analysis
CreateCrcBiomeScreenObjectFromTSE | Create a CrcBiomeScreen object from TreeSummarizedExperiment
EvaluateCrcBiomeScreen | Evaluate the performance of model predictions
EvaluateModel | Evaluate the model to select the optimal model
EvaluateRF | Evaluate the Random Forest model
EvaluateXGBoost | Evaluate the XGBoost model
FilterDataSet | Filter the CrcBiomeScreenObject dataset based on a specific label
getAbsoluteAbundance | Accessor for AbsoluteAbundance slot of CrcBiomeScreen object
getAbsoluteAbundance-method | Accessor for AbsoluteAbundance slot of CrcBiomeScreen object
getModelData | Accessor for ModelData slot of CrcBiomeScreen object
getModelData-method | Accessor for SampleData slot of CrcBiomeScreen object
getModelResult | Accessor for ModelResult slot of CrcBiomeScreen object
getModelResult-method | Accessor for ModelResult slot of CrcBiomeScreen object
getNormalizedData | Accessor for NormalizedData slot of CrcBiomeScreen object
getNormalizedData-method | Accessor for NormalizedData slot of CrcBiomeScreen object
getOutlierSamples | Accessor for OutlierSamples
getOutlierSamples-method | Accessor for OutlierSamples
getPredictResult | Accessor for PredictResult slot of CrcBiomeScreen object
getPredictResult-method | Accessor for PredictResult slot of CrcBiomeScreen object
getRelativeAbundance | Accessor for RelativeAbundance slot of CrcBiomeScreen object
getRelativeAbundance-method | Accessor for RelativeAbundance slot of CrcBiomeScreen object
getSampleData | Accessor for SampleData slot of CrcBiomeScreen object
getSampleData-method | Accessor for SampleData slot of CrcBiomeScreen object
getTaxaData | Accessor for TaxaData slot of CrcBiomeScreen object
getTaxaData-method | Accessor for TaxaData slot of CrcBiomeScreen object
getTaxaLevelData | Accessor for TaxaLevelData slot
getTaxaLevelData-method | Accessor for TaxaLevelData slot
KeepTaxonomicLevel | Summarize abundance data at a given taxonomic level
LoadTaxaTable | Load a custom taxa table for ASV/OTU data
ModelingRF | The packaging function for Random Forest modeling
ModelingRF_noweights | The function for modeling random forest without using class weights
ModelingXGBoost | The packaging function for XGBoost modeling
ModelingXGBoost_noweights | The packaging function for XGBoost modeling without using class weights
NHSBCSP_screeningData | NHSBCSP screening dataset
NormalizeData | Normalise the absolute data to relative data by using Total Sum Scaling and Geometric Mean of Pairwise Ratios (GMPR)
PredictCrcBiomeScreen | Predict the class and probabilities for new data
qcByCmdscale | Quality control using classical MDS and outlier detection
RunScreening | Run the screening process for the microbiome data
setNormalizedData-setter | setNormalizedData<-: Setter for NormalizedData slot of CrcBiomeScreen object
setNormalizedData<- | setNormalizedData<-: Setter for NormalizedData slot of CrcBiomeScreen object
setNormalizedData<--method | setNormalizedData<-: Setter for NormalizedData slot of CrcBiomeScreen object
setTaxaData-setter | setTaxaData<-: Setter for TaxaData slot of CrcBiomeScreen object
setTaxaData<- | setTaxaData<-: Setter for TaxaData slot of CrcBiomeScreen object
setTaxaData<--method | setTaxaData<-: Setter for TaxaData slot of CrcBiomeScreen object
SplitDataSet | Split the dataset into training and test sets
SplitTaxas | Split and clean taxonomy strings
Thomas_2018_RelativeAbundance | Thomas 2018 relative abundance dataset
TrainModels | Train the different models
ValidateModelOnData | Predict the validation data by using the trained model in CrcBiomeScreenObject
ZellerG_2014_RelativeAbundance | Zeller 2014 relative abundance dataset