Package: beer 1.11.0

Athena Chen

beer: Bayesian Enrichment Estimation in R

BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data. Given a PhIPData object, BEER returns posterior probabilities of enriched antibody responses, point estimates for the relative fold-change in comparison to negative control samples, and more. Additionally, BEER provides a convenient implementation for using edgeR to identify enriched antibody responses.

Authors:Athena Chen [aut, cre], Rob Scharpf [aut], Ingo Ruczinski [aut]

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NEWS

# Install 'beer' in R:
install.packages('beer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/athchen/beer/issues

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3

On BioConductor:beer-1.9.0(bioc 3.20)beer-1.8.0(bioc 3.19)

softwarestatisticalmethodbayesiansequencingcoverage

5.33 score 9 stars 12 scripts 152 downloads 10 exports 77 dependencies

Last updated 23 days agofrom:a025d0bab3. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winOKOct 30 2024
R-4.4-macOKOct 30 2024
R-4.3-winOKOct 30 2024
R-4.3-macOKOct 30 2024

Exports:beadsRRbrewbrewOneedgeROneedgeROneQLFgetABgetBFgetExpectedguessEnrichedrunEdgeR

Dependencies:abindaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobcachemclicodacodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdplyredgeRfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslPhIPDatapillarpkgconfigplogrprogressrpurrrR6rjagsrlangRSQLiteS4ArraysS4VectorssnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc

Estimating Enrichment in PhIP-Seq Experiments with BEER

Athena Chen, Kai Kammers, Rob Scharpf, Ingo Ruczinski

Rendered frombeer.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-06-27
Started: 2021-02-23

Readme and manuals

Help Manual

Help pageTopics
Function to run the beads-only round robin using BEER.beadsRRBeer
Function to run the beads-only round robin using edgeR.beadsRREdgeR
Run BEER for all samples.brewSamples
Function to check that the counts matrix only contains integers.checkCounts
Function to check whether an assay will be overwritten.checkOverwrite
Estimate edgeR dispersion parameters from the beads-only data using qCML.edgeRBeads
Estimate edgeR dispersion parameters from the beads-only samples using Cox-Reid profile adjusted likelihood method for estimating dispersions..edgeRBeadsQLF
Derive beta shape parameters using edgeR dispersion estimates.getABEdgeR
Wrapper function to derive MLE estimates of a, b from beads-only samples.getABMLE
Helper function to derive MLE estimates of a, b from a vector of proportions.getABMLEProp
Wrapper function to derive MOM estimates of a, b from beads-only samples.getABMOM
Helper function to derive MOM estimates of a, b from a vector of proportions.getABMOMProp
Guess super-enriched peptides based on edgeR fold-change estimates.guessEnrichedEdgeR
Guess enriched peptides based on MLE estimates of the true fold-change.guessEnrichedMLE
Clean-up specified assay names.tidyAssayNames
Clean inputs for JAGS parameters.tidyInputsJAGS
Clean up inputs for prior estimation.tidyInputsPrior
Clean up inputs for identifying super-enriched peptides.tidyInputsSE
Beads-only round robinbeadsRR
Bayesian Enrichment Estimation in R (BEER)brew
Run BEER for one samplebrewOne
Run edgeR for one sample against all the beads-only samples.edgeROne
Run edgeR for one sample against all the beads-only samples using edgeR's QLF Test for differential expression.edgeROneQLF
Estimate beads-only shape parametersgetAB
Calculate Bayes FactorsgetBF
Calculate expected read counts or proportion of readsgetExpected
Identifying clearly enriched peptidesguessEnriched
Derive initial estimates of unknown model parametersguessInits
Run edgeR on PhIP-Seq datarunEdgeR
Summarize MCMC chain and return point estimates for BEER parameterssummarizeRun
Derive point estimates for c, pi, phi, and Z for a particular samplesummarizeRunOne