Package: AWAggregator
Type: Package
Title: Attribute-Weighted Aggregation
Version: 1.0.0
Authors@R: 
    c(
        person(given = "Jiahua",
            family = "Tan",
            email = "jiahuatan@chem.ubc.ca",
            role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5839-1049")
        ),
        person(given = "Gian L.",
            family = "Negri",
            email = "gnegri@bcgsc.ca",
            role = c("aut"),
            comment = c(ORCID = "0000-0001-7722-8888")
        ),
        person(given = "Gregg B.",
            family = "Morin",
            email = "gmorin@bcgsc.ca",
            role = c("aut"),
            comment = c(ORCID = "0000-0001-8949-4374")
        ),
        person(given = "David D. Y.",
            family = "Chen",
            email = "chen@chem.ubc.ca",
            role = c("aut"),
            comment = c(ORCID = "0000-0002-3669-6041")
        )
    )
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Suggests: AWAggregatorData, BiocStyle, ExperimentHub, knitr, rmarkdown,
        testthat (>= 3.0.0)
Imports: dplyr, Peptides, progress, purrr, ranger, rlang, stats,
        stringr, tidyr, toOrdinal, utils
Depends: R (>= 4.5.0)
biocViews: Software, MassSpectrometry, Preprocessing, Proteomics,
        Regression
BugReports: https://github.com/Tan-Jiahua/AWAggregator/issues
URL: https://github.com/Tan-Jiahua/AWAggregator
VignetteBuilder: knitr
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/AWAggregator
git_branch: RELEASE_3_22
git_last_commit: 8fdf64b
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 02:54:41 UTC; biocbuild
Author: Jiahua Tan [aut, cre] (ORCID: <https://orcid.org/0000-0001-5839-1049>),
  Gian L. Negri [aut] (ORCID: <https://orcid.org/0000-0001-7722-8888>),
  Gregg B. Morin [aut] (ORCID: <https://orcid.org/0000-0001-8949-4374>),
  David D. Y. Chen [aut] (ORCID: <https://orcid.org/0000-0002-3669-6041>)
Maintainer: Jiahua Tan <jiahuatan@chem.ubc.ca>
Built: R 4.5.1; ; 2025-10-30 12:04:37 UTC; unix
