.mbecGetData            Mbec-Data Getter
.mbecGetPhyloseq        Return Phyloseq after correction
.mbecSetData            Mbec-Data Setter
MBECS                   MBECS: Evaluation and correction of batch
                        effects in microbiome data-sets.
MbecData                Define MbecData-class
colinScore              Variable Correlation Linear (Mixed) Models
dummy.list              Mock-up microbiome abundance table and
                        meta-data.
dummy.mbec              Mock-up microbiome abundance table and
                        meta-data.
dummy.ps                Mock-up microbiome abundance table and
                        meta-data.
externalPLSDA           Partial Least Squares Discriminant Analysis
                        Computation
mbecBMC                 Batch Mean Centering (BMC)
mbecBat                 Combat Batch Effects (ComBat)
mbecBox                 Feature Differential Abundance Box-Plot
mbecBoxPlot             Variability boxes plotting function
mbecCLR                 Centered Log-Ratio Transformation
mbecCorrection          Batch Effect Correction Wrapper
mbecDeflate             Calculate matrix residuals
mbecDummy               Creates a dummy data-set with abundance matrix
                        and meta-data.
mbecExplainedVariance   Calculate explained variance using CCA
mbecGetData             Mbec-Data Getter
mbecGetData,MbecData-method
                        Mbec-Data Getter
mbecGetPhyloseq         Return Phyloseq after correction
mbecGetPhyloseq,MbecData-method
                        Return Phyloseq after correction
mbecHeat                Feature Differential Abundance Heatmap
mbecHeatPlot            Heatmap plotting function
mbecHelpFactor          Check If Covariates Are Factors
mbecLM                  Linear (Mixed) Model Feature to Batch Fit
mbecMixedVariance       Mixed Model Variance-Component Extraction
mbecModelVariance       Estimate Explained Variance
mbecModelVarianceLM     Estimate Explained Variance with Linear Models
mbecModelVarianceLMM    Estimate Explained Variance with Linear Mixed
                        Models
mbecModelVariancePVCA   Estimate Explained Variance with Principal
                        Variance Component Analysis
mbecModelVarianceRDA    Estimate Explained Variance with Redundancy
                        Analysis
mbecModelVarianceSCOEF
                        Estimate Explained Variance with Silhouette
                        Coefficient
mbecMosaic              Mosaic Sample Group Allocation
mbecMosaicPlot          Mosaic plotting function
mbecPCA                 Principal Component Analysis Plot
mbecPCA,MbecData-method
                        Principal Component Analysis Plot for MbecData
mbecPCAPlot             PCA plotting function
mbecPLSDA               Partial Least Squares Discriminant Analysis
mbecPN                  Percentile Normalization (PN)
mbecPVCAStatsPlot       Plot Proportion of Variance for PVCA
mbecProcessInput        Mbec-Data Constructor Wrapper
mbecProcessInput,MbecData-method
                        Mbec-Data Constructor Wrapper
mbecProcessInput,list-method
                        Mbec-Data Constructor Wrapper
mbecProcessInput,phyloseq-method
                        Mbec-Data Constructor Wrapper
mbecRBE                 Remove Batch Effects (RBE)
mbecRDAStatsPlot        Plot Proportion of Variance for pRDA
mbecRLE                 Relative Log Expression Plot
mbecRLEPlot             RLE plotting function
mbecRUV2                Remove unwanted Variation 2 (RUV-2)
mbecRUV3                Remove Unwanted Variation 3 (RUV-3)
mbecRUV4                Remove Unwanted Variation 4 (RUV-4)
mbecReportPost          Constructs a comparative report of batch
                        corrected data.
mbecReportPrelim        Constructs an initial report of a single
                        data-set.
mbecRunCorrections      Run Correction Pipeline
mbecSCOEFStatsPlot      Plot Silhouette Coefficient
mbecSVA                 Surrogate variable Analysis (SVA)
mbecSVD                 Singular Value Decomposition (SVD)
mbecSetData             Mbec-Data Setter
mbecSetData,MbecData-method
                        Mbec-Data Setter
mbecTestModel           Check If Model Is Estimable
mbecTransform           Normalizing Transformations
mbecUpperCase           Capitalize Word Beginning
mbecValidateModel       Validate Linear (Mixed) Models
mbecVarianceStats       Wrapper for Model Variable Variance Extraction
mbecVarianceStatsLM     Model Variable Variance Extraction from LM
mbecVarianceStatsLMM    Model Variable Variance Extraction from LMM
mbecVarianceStatsPlot   Plot Proportion of Variance for L(M)M
percentileNorm          Percentile Normalization
poscore                 Percentile of Score
