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AWAggregator
This is thereleased version of AWAggregator; for the devel version, seeAWAggregator.
Attribute-Weighted Aggregation
Bioconductor version: Release (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("AWAggregator")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("AWAggregator")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("AWAggregator")| AWAggregator vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | MassSpectrometry,Preprocessing,Proteomics,Regression,Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | MIT + fileLICENSE |
| 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 |
See More
| Suggests | AWAggregatorData,BiocStyle,ExperimentHub,knitr,rmarkdown,testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | AWAggregator_1.0.0.tar.gz |
| Windows Binary (x86_64) | AWAggregator_1.0.0.zip |
| macOS Binary (x86_64) | AWAggregator_1.0.0.tgz |
| macOS Binary (arm64) | AWAggregator_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/AWAggregator |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/AWAggregator |
| Bioc Package Browser | https://code.bioconductor.org/browse/AWAggregator/ |
| Package Short Url | https://bioconductor.org/packages/AWAggregator/ |
| Package Downloads Report | Download Stats |