Package: beer 1.9.0

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]

beer_1.9.0.tar.gz
beer_1.9.0.zip(r-4.5)beer_1.9.0.zip(r-4.4)beer_1.9.0.zip(r-4.3)
beer_1.9.0.tgz(r-4.4-any)beer_1.9.0.tgz(r-4.3-any)
beer_1.9.0.tar.gz(r-4.5-noble)beer_1.9.0.tar.gz(r-4.4-noble)
beer_1.9.0.tgz(r-4.4-emscripten)beer_1.9.0.tgz(r-4.3-emscripten)
beer.pdf |beer.html✨
beer/json (API)
NEWS

# Install 'beer' in R:

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

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)

bioconductor-package

10 exports 0.61 score 78 dependencies

Last updated 2 months agofrom:a5ffae4270

Exports:beadsRR brew brewOne edgeROne edgeROneQLF getAB getBF getExpected guessEnriched runEdgeR

Dependencies:abind askpass BH Biobase BiocFileCache BiocGenerics BiocParallel bit bit64 blob cachem cli coda codetools cpp11 crayon curl DBI dbplyr DelayedArray digest dplyr edgeR fansi fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges jsonlite lambda.r lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mime openssl PhIPData pillar pkgconfig plogr progressr purrr R6 Rcpp rjags rlang RSQLite S4Arrays S4Vectors snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr XVector zlibbioc

Estimating Enrichment in PhIP-Seq Experiments with BEER

Athena Chen, Kai Kammers, Rob Scharpf, Ingo Ruczinski

Rendered frombeer.Rmdusingknitr::rmarkdownon Jun 30 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 robin	beadsRR
Bayesian Enrichment Estimation in R (BEER)	brew
Run BEER for one sample	brewOne
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 parameters	getAB
Calculate Bayes Factors	getBF
Calculate expected read counts or proportion of reads	getExpected
Identifying clearly enriched peptides	guessEnriched
Derive initial estimates of unknown model parameters	guessInits
Run edgeR on PhIP-Seq data	runEdgeR
Summarize MCMC chain and return point estimates for BEER parameters	summarizeRun
Derive point estimates for c, pi, phi, and Z for a particular sample	summarizeRunOne