Package: MBECS 1.17.0

Michael Olbrich

MBECS: Evaluation and correction of batch effects in microbiome data-sets

The Microbiome Batch Effect Correction Suite (MBECS) provides a set of functions to evaluate and mitigate unwated noise due to processing in batches. To that end it incorporates a host of batch correcting algorithms (BECA) from various packages. In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects.

Authors:Michael Olbrich [aut, cre]

MBECS_1.17.0.tar.gz
MBECS_1.17.0.zip(r-4.7-any)MBECS_1.17.0.zip(r-4.6-any)MBECS_1.17.0.zip(r-4.5-any)
MBECS_1.17.0.tgz(r-4.6-any)MBECS_1.17.0.tgz(r-4.5-any)
MBECS_1.17.0.tar.gz(r-4.7-any)MBECS_1.17.0.tar.gz(r-4.6-any)
MBECS_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MBECS/json (API)

# Install 'MBECS' in R:

install.packages('MBECS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rmolbrich/mbecs/issues

Datasets:

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.

On BioConductor:MBECS-1.17.0(bioc 3.24)MBECS-1.16.0(bioc 3.23)

batcheffect microbiome reportwriting visualization normalization qualitycontrol

4.60 score 4 stars 8 scripts 433 downloads 38 exports 128 dependencies

Last updated from:87f397a1dd. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	177
linux-devel	NOTE	412
source / vignettes	OK	295
linux-release	NOTE	368
macos-release	NOTE	271
macos-oldrel	NOTE	246
windows-devel	NOTE	287
windows-release	NOTE	291
windows-oldrel	NOTE	285
wasm-release	OK	210

Exports:.mbecGetData .mbecGetPhyloseq .mbecSetData colinScore mbecBox mbecBoxPlot mbecCorrection MbecData mbecDummy mbecGetData mbecGetPhyloseq mbecHeat mbecHeatPlot mbecHelpFactor mbecLM mbecMixedVariance mbecModelVariance mbecMosaic mbecMosaicPlot mbecPCA mbecPCAPlot mbecProcessInput mbecPVCAStatsPlot mbecRDAStatsPlot mbecReportPost mbecReportPrelim mbecRLE mbecRLEPlot mbecRunCorrections mbecSCOEFStatsPlot mbecSetData mbecTestModel mbecTransform mbecValidateModel mbecVarianceStats mbecVarianceStatsPlot percentileNorm poscore

Dependencies:ade4 annotate AnnotationDbi ape askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocParallel biomformat Biostrings bit bit64 blob boot bslib cachem cli cluster codetools cpp11 crayon curl data.table DBI digest dplyr edgeR evaluate farver fastmap fontawesome foreach formatR fs futile.logger futile.options genefilter generics ggplot2 glue gridExtra gtable highr htmltools httr igraph IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle limma lme4 lmerTest locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime minqa multtest nlme nloptr numDeriv openssl permute pheatmap phyloseq pillar pixmap pkgconfig plyr png purrr R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas reshape2 rlang rmarkdown RSQLite ruv S4Vectors S7 sass scales Seqinfo snow sp statmod stringi stringr survival sva sys tibble tidyr tidyselect tinytex utf8 vctrs vegan viridisLite withr xfun XML xtable XVector yaml

MBECS introduction

Rendered frommbecs_vignette.Rmdusingknitr::knitr

Last update: 2022-02-22
Started: 2021-11-09

Citation

Development and contributors

Readme and manuals

Help Manual

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