AWAggregator

This is the development version of AWAggregator; to use it, please install the devel version of Bioconductor.

Attribute-Weighted Aggregation

Bioconductor version: Development (3.22)

This package implements an attribute-weighted aggregation algorithm which leverages peptide-spectrum match (PSM) attributes to provide a more accurate estimate of protein abundance compared to conventional aggregation methods. This algorithm employs pre-trained random forest models to predict the quantitative inaccuracy of PSMs based on their attributes. PSMs are then aggregated to the protein level using a weighted average, taking the predicted inaccuracy into account. Additionally, the package allows users to construct their own training sets that are more relevant to their specific experimental conditions if desired.

Author: Jiahua Tan [aut, cre] ORCID: 0000-0001-5839-1049 , Gian L. Negri [aut] ORCID: 0000-0001-7722-8888 , Gregg B. Morin [aut] ORCID: 0000-0001-8949-4374 , David D. Y. Chen [aut] ORCID: 0000-0002-3669-6041

Maintainer: Jiahua Tan <jiahuatan at chem.ubc.ca>

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("AWAggregator")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	MassSpectrometry, Preprocessing, Proteomics, Regression, Software
Version	0.99.4
In Bioconductor since	BioC 3.22 (R-4.5)
License	MIT + file LICENSE
Depends	R (>= 4.5.0)
Imports	dplyr, Peptides, progress, purrr, ranger, rlang, stats, stringr, tidyr, toOrdinal, utils
System Requirements
URL	https://github.com/Tan-Jiahua/AWAggregator
Bug Reports	https://github.com/Tan-Jiahua/AWAggregator/issues

Suggests	AWAggregatorData, BiocStyle, ExperimentHub, knitr, rmarkdown, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/AWAggregator
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/AWAggregator
Package Short Url	https://bioconductor.org/packages/AWAggregator/
Package Downloads Report	Download Stats