pgca

DOI: 10.18129/B9.bioc.pgca  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see pgca.

PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data

Bioconductor version: 3.16

Protein Group Code Algorithm (PGCA) is a computationally inexpensive algorithm to merge protein summaries from multiple experimental quantitative proteomics data. The algorithm connects two or more groups with overlapping accession numbers. In some cases, pairwise groups are mutually exclusive but they may still be connected by another group (or set of groups) with overlapping accession numbers. Thus, groups created by PGCA from multiple experimental runs (i.e., global groups) are called "connected" groups. These identified global protein groups enable the analysis of quantitative data available for protein groups instead of unique protein identifiers.

Author: Gabriela Cohen-Freue <gcohen at stat.ubc.ca>

Maintainer: Gabriela Cohen-Freue <gcohen at stat.ubc.ca>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("pgca")

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("pgca")

 

HTML	R Script	Introduction
PDF		Reference Manual

Details

biocViews	AssayDomain, ImmunoOncology, MassSpectrometry, Proteomics, Software, WorkflowStep
Version	1.22.0
In Bioconductor since	BioC 3.5 (R-3.4) (6 years)
License	GPL (>= 2)
Depends
Imports	utils, stats
LinkingTo
Suggests	knitr, testthat, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	pgca_1.22.0.tar.gz
Windows Binary	pgca_1.22.0.zip
macOS Binary (x86_64)	pgca_1.22.0.tgz
macOS Binary (arm64)	pgca_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pgca
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pgca
Bioc Package Browser	https://code.bioconductor.org/browse/pgca/
Package Short Url	https://bioconductor.org/packages/pgca/
Package Downloads Report	Download Stats