.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. |
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 |
mbecDummy | Creates a dummy data-set with abundance matrix and meta-data. |
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 |
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 |
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 |