Evaluation and correction of batch effects in microbiome data-sets

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Documentation for package ‘MBECS’ version 1.9.0

• 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