Man pages for buschlab/MBECS
Evaluation and correction of batch effects in microbiome data-sets
| colinScore | Variable Correlation Linear (Mixed) Models |
| dot-mbecGetData | Mbec-Data Getter |
| dot-mbecSetData | Mbec-Data Setter |
| 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 |
| mbecGetData | Mbec-Data Getter |
| mbecGetData-MbecData-method | Mbec-Data Getter |
| 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... |
| 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 |
| mbecPN | Percentile Normalization (PN) |
| mbecProcessInput | Mbec-Data Constructor Wrapper |
| mbecProcessInput-list-method | Mbec-Data Constructor Wrapper |
| mbecProcessInput-MbecData-method | Mbec-Data Constructor Wrapper |
| mbecProcessInput-phyloseq-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 an initial report of a single data-set without... |
| mbecReportPrelim | Constructs an initial report of a single data-set without... |
| 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) |
| mbecSCOEFStatsPlot | Plot Silhouette Coefficient |
| mbecSetData | Mbec-Data Setter |
| mbecSetData-MbecData-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 |
| pipe | Pipe operator |
| poscore | Percentile of Score |
