Package: bppg 0.99.1

Karin Schork

bppg: Bipartite peptide-protein graphs

This package contains functionality to create and characterize bipartite graphs that model the relationship between peptides and proteins in bottom-up proteomics. With these graphs, protein ratios (fold change between two sample groups) are calculated from the respective measured peptide ratios. The main aim is to make use of quantitative information contained in shared peptides and making it possible to quantify proteins without shared peptides. Further, the package offers general analysis of peptide and protein relationships using bipartite graphs and visualization for these graphs.

Authors:Karin Schork [aut, cre], Julika Wenzel [aut], Katharina Neuhaus [aut], Martin Eisenacher [aut, fnd]

bppg_0.99.1.tar.gz
bppg_0.99.1.zip(r-4.7-any)bppg_0.99.1.zip(r-4.6-any)bppg_0.99.1.zip(r-4.5-any)
bppg_0.99.1.tgz(r-4.6-any)bppg_0.99.1.tgz(r-4.5-any)
bppg_0.99.1.tar.gz(r-4.7-any)bppg_0.99.1.tar.gz(r-4.6-any)
bppg_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bppg/json (API)

# Install 'bppg' in R:

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

Bug tracker:https://github.com/mpc-bioinformatics/bppg/issues

On CRAN:

proteomics graphandnetwork massspectrometry multiplecomparison visualization

4.08 score 1 scripts 16 exports 88 dependencies

Last updated from:e3f64d0f75. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	190
linux-devel	OK	263
source / vignettes	OK	331
linux-release	OK	336
macos-release	OK	268
macos-oldrel	OK	214
windows-devel	OK	268
windows-release	OK	259
windows-oldrel	OK	254
wasm-release	OK	133

Exports:aggregateReplicates automatedAnalysisIteratedCi calculatePeptideRatios combineComparisons digestFASTA exportSE generateGraphsFromEdgelist generateGraphsFromFASTA generateGraphsFromQuantData generateQuantGraphs iterateOverCi normalizePeptideIntensities plotBipartiteGraph proteinElimination readFpPeptideTable readMqPeptideTable

Dependencies:abind affy affyio backports base64enc Biobase BiocGenerics BiocManager cachem checkmate cli codetools cpp11 DelayedArray DEoptimR digest dplyr farver fastmap future future.apply generics GenomicRanges ggforce ggplot2 ggraph ggrepel globals glue graphlayouts gridExtra gtable igraph IRanges isoband jsonlite labeling lattice lifecycle limma listenv magrittr MASS Matrix MatrixGenerics matrixStats memoise numDeriv openxlsx parallelly pbapply pillar pkgconfig polyclip preprocessCore purrr R6 RColorBrewer Rcpp RcppArmadillo rlang robustbase Rsolnp S4Arrays S4Vectors S7 scales Seqinfo SparseArray statmod stringi stringr SummarizedExperiment systemfonts tibble tidygraph tidyr tidyselect truncnorm tweenr utf8 vctrs viridis viridisLite vsn withr XVector zip

Introduction to BPPG

Rendered frombppg.Rmdusingknitr::rmarkdown

Last update: 2026-08-12
Started: 2026-04-29

Help page	Topics
Adds vertex attributes with uniqueness of peptides and number of unique peptides for proteins.	.addUniquenessAttributes
Analyse results for a single protein	.analyseResultSingleProt
Calculate equality and inequality constraints for the optimization step	.calcConstraints
Calculate objective function for the optimization step	.calcObjectiveFunction
Calculate optimal solution for a single gridpoint	.calcResultGridpoint
Cleavage of a single protein sequence.	.cleave
Contracting of peptide and protein nodes.	.contractGraph
Digestion of a single protein sequence.	.digest2
Transform a bipartite graph into a directed graph.	.directBipartiteGraph
Function to set up the error equations for the optimization problem	.errorEquation
Helper function that extracts the intensity columns and columns of interest from a given dataframe.	.extractIntensities
Calculate peptide ratios for pairwise comparisons of groups (Y/X).	.foldChange
Calculate the geometric mean.	.geomMean
Create Mapping signature for igraph::contract function.	.getContractMapping
Calulate initial values for Ci (protein weights) for optimization	.initializeCi
Calulate initial values for Ri (protein ratios) for optimization	.initializeRi
Enchanced version of the igraph::isomorphic function that also considers the node type in bipartite graphs, e.g. that W- and M-shaped graphs are NOT isomorphic	.isomorphicBipartite
Function to set up the optimization problem and minimize the sum of squared error terms	.minimizeSquaredError
Set names for plotting with plotBipartiteGraph.	.setNodeLabels
Funktion to format Tracking information into a dataframe with columnnames.	.trackingDataFrame
Aggregate replicates of the same experimental group.	aggregateReplicates
Extract protein ratio solutions from the result of iterateOverCi()	automatedAnalysisIteratedCi
Calculation of peptide ratios from aggregated intensities.	calculatePeptideRatios
Combine relative quantification results over multiple pairwise comparisons into a single SummarizedExperiments object.	combineComparisons
In silico tryptic digestion of whole FASTA file.	digestFASTA
Export SummarizedExperiment object to an Excel file, with one assay per sheet.	exportSE
Generate bipartite peptide-protein graphs from a list of digested proteins via an edgelist. Peptide and protein nodes can be contracted.	generateGraphsFromEdgelist
Generate graphs from a FASTA file	generateGraphsFromFASTA
Generate graphs from quantitative peptide-level data	generateGraphsFromQuantData
Generate graphs from peptide ratio table, using an edgelist calculated on the fasta file.	generateQuantGraphs
Iterate over possible Ci values	iterateOverCi
Normalization of peptide intensities	normalizePeptideIntensities
Plotting of bipartite peptide-protein graphs.	plotBipartiteGraph
Tries to recursively remove protein nodes from graph while keeping the error term in the optimization step low	proteinElimination
Import of FragPipe's combined_peptide.tsv-table.	readFpPeptideTable
Import of MaxQuant's peptide.txt-table.	readMqPeptideTable

Package: bppg 0.99.1

bppg: Bipartite peptide-protein graphs

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