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IsoBayes

IsoBayes: Single Isoform protein inference Method via Bayesian Analyses


Bioconductor version: Release (3.18)

IsoBayes is a Bayesian method to perform inference on single protein isoforms. Our approach infers the presence/absence of protein isoforms, and also estimates their abundance; additionally, it provides a measure of the uncertainty of these estimates, via: i) the posterior probability that a protein isoform is present in the sample; ii) a posterior credible interval of its abundance. IsoBayes inputs liquid cromatography mass spectrometry (MS) data, and can work with both PSM counts, and intensities. When available, trascript isoform abundances (i.e., TPMs) are also incorporated: TPMs are used to formulate an informative prior for the respective protein isoform relative abundance. We further identify isoforms where the relative abundance of proteins and transcripts significantly differ. We use a two-layer latent variable approach to model two sources of uncertainty typical of MS data: i) peptides may be erroneously detected (even when absent); ii) many peptides are compatible with multiple protein isoforms. In the first layer, we sample the presence/absence of each peptide based on its estimated probability of being mistakenly detected, also known as PEP (i.e., posterior error probability). In the second layer, for peptides that were estimated as being present, we allocate their abundance across the protein isoforms they map to. These two steps allow us to recover the presence and abundance of each protein isoform.

Author: Jordy Bollon [aut], Simone Tiberi [aut, cre]

Maintainer: Simone Tiberi <simone.tiberi at unibo.it>

Citation (from within R, enter citation("IsoBayes")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("IsoBayes")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("IsoBayes")
IsoBayes HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews AlternativeSplicing, Bayesian, GeneExpression, Genetics, MassSpectrometry, Proteomics, RNASeq, Sequencing, Software, StatisticalMethod, Visualization
Version 1.0.1
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License GPL-3
Depends R (>= 4.3.0)
Imports methods, Rcpp, data.table, glue, stats, doParallel, parallel, doRNG, foreach, iterators, ggplot2, HDInterval, SummarizedExperiment, S4Vectors
System Requirements C++17
URL https://github.com/SimoneTiberi/IsoBayes
Bug Reports https://github.com/SimoneTiberi/IsoBayes/issues
See More
Suggests knitr, rmarkdown, testthat, BiocStyle
Linking To Rcpp, RcppArmadillo
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package IsoBayes_1.0.1.tar.gz
Windows Binary IsoBayes_1.0.1.zip
macOS Binary (x86_64) IsoBayes_1.0.1.tgz
macOS Binary (arm64) IsoBayes_1.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/IsoBayes
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/IsoBayes
Bioc Package Browser https://code.bioconductor.org/browse/IsoBayes/
Package Short Url https://bioconductor.org/packages/IsoBayes/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive