# Evaluation and correction of batch effects in microbiome data-sets

## Documentation for package ‘MBECS’ version 1.14.0

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

## Help Pages

.mbecGetData | Mbec-Data Getter
.mbecGetPhyloseq | Return Phyloseq after correction
.mbecSetData | Mbec-Data Setter
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
mbecBat | Combat Batch Effects (ComBat)
mbecBMC | Batch Mean Centering (BMC)
mbecBox | Feature Differential Abundance Box-Plot
mbecBoxPlot | Variability boxes plotting function
mbecCLR | Centered Log-Ratio Transformation
mbecCorrection | Batch Effect Correction Wrapper
MbecData | Define MbecData-class
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-method | Mbec-Data Getter
mbecGetPhyloseq | Return Phyloseq after correction
mbecGetPhyloseq-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-method | Principal Component Analysis Plot for MbecData
mbecPCAPlot | PCA plotting function
mbecPLSDA | Partial Least Squares Discriminant Analysis
mbecPN | Percentile Normalization (PN)
mbecProcessInput | Mbec-Data Constructor Wrapper
mbecProcessInput-method | Mbec-Data Constructor Wrapper
mbecProcessInput-method | Mbec-Data Constructor Wrapper
mbecProcessInput-method | Mbec-Data Constructor Wrapper
mbecPVCAStatsPlot | Plot Proportion of Variance for PVCA
mbecRBE | Remove Batch Effects (RBE)
mbecRDAStatsPlot | Plot Proportion of Variance for pRDA
mbecReportPost | Constructs a comparative report of batch corrected data.
mbecReportPrelim | Constructs an initial report of a single data-set.
mbecRLE | Relative Log Expression Plot
mbecRLEPlot | RLE plotting function
mbecRunCorrections | Run Correction Pipeline
mbecRUV2 | Remove unwanted Variation 2 (RUV-2)
mbecRUV3 | Remove Unwanted Variation 3 (RUV-3)
mbecRUV4 | Remove Unwanted Variation 4 (RUV-4)
MBECS | MBECS: Evaluation and correction of batch effects in microbiome data-sets.
mbecSCOEFStatsPlot | Plot Silhouette Coefficient
mbecSetData | Mbec-Data Setter
mbecSetData-method | Mbec-Data Setter
mbecSVA | Surrogate variable Analysis (SVA)
mbecSVD | Singular Value Decomposition (SVD)
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