Package: PCAPAM50
Type: Package
Title: Enhanced 'PAM50' Subtyping of Breast Cancer
Version: 1.0.4
Authors@R: c(person("Praveen-Kumar", "Raj-Kumar", role = c("aut", "cre", "cph"), email = "p.rajkumar@wriwindber.org"), person("Boyi", "Chen", role = "aut"), person("Ming-Wen", "Hu", role = "aut"), person("Tyler", "Hohenstein", role = "aut"), person("Jianfang", "Liu", role = "aut"), person("Craig D.", "Shriver", role = "aut"), person("Xiaoying", "Lin", role = c("aut", "cph")), person("Hai", "Hu", role = c("aut", "cph")))
Maintainer: Praveen-Kumar Raj-Kumar <p.rajkumar@wriwindber.org>
Description: Accurate classification of breast cancer tumors based on
        gene expression data is not a trivial task, and it lacks
        standard practices.The 'PAM50' classifier, which uses 50 gene
        centroid correlation distances to classify tumors, faces
        challenges with balancing estrogen receptor (ER) status and
        gene centering. The 'PCAPAM50' package leverages principal
        component analysis and iterative 'PAM50' calls to create a gene
        expression-based ER-balanced subset for gene centering,
        avoiding the use of protein expression-based ER data resulting
        into an enhanced Breast Cancer subtyping. The PCA-PAM50 method
        is described in Raj-Kumar et al. (2019)
        <https://www.nature.com/articles/s41598-019-44339-4> and the
        package implementation is described in Raj-Kumar et al. (2026)
        <https://www.nature.com/articles/s41598-025-30752-5>.
License: GPL (>= 3)
Copyright: 2024 Windber Research Institute, Windber, PA - 15963. All
        Rights Reserved.
Encoding: UTF-8
Suggests: testthat, knitr, rmarkdown
Config/testthat/edition: 3
RoxygenNote: 7.2.3
Imports: Biobase, lattice, ComplexHeatmap, impute
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-10-16 10:26:22 UTC; root
Author: Praveen-Kumar Raj-Kumar [aut, cre, cph], Boyi Chen [aut],
        Ming-Wen Hu [aut], Tyler Hohenstein [aut], Jianfang Liu [aut],
        Craig D. Shriver [aut], Xiaoying Lin [aut, cph], Hai Hu [aut,
        cph]
Config/pak/sysreqs: libpng-dev perl
Repository: https://rajkumpismb.r-universe.dev
Date/Publication: 2026-07-30 17:00:12 UTC
RemoteUrl: https://github.com/cran/PCAPAM50
RemoteRef: HEAD
RemoteSha: 8920f64bb7cc669c1cd1fe09370aaa6029877118