Package: spqrp
Title: Sample Provenance Quality Resolver in Proteomics
Version: 0.1.0
Authors@R: c(
    person("Franziska", "Hradilak",
           email = "Franziska.Hradilak@student.hpi.uni-potsdam.de",
           role = c("aut", "cre")))
Description: Detect sample-provenance inconsistencies and potential mix-ups in mass-spectrometry-based
    plasma-proteome cohorts. Provides a clustering-based approach (build a
    nearest-neighbour graph in a dimensionality-reduced space and iteratively
    split large components by edge weight), a threshold-based approach
    (classify sample pairs as belonging or not-belonging from a pairwise
    distance cutoff), parameter optimization over distance metrics and
    cutoffs, and a pairwise random-forest classifier for protein importance
    ranking. This is a native R port of the author's Python package
    'spqrp' (<https://github.com/fhradilak/spqrp>), implementing methods from an associated manuscript currently in preparation.
License: GPL-3
URL: https://github.com/fhradilak/spqrp_r
BugReports: https://github.com/fhradilak/spqrp_r/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.5.0)
Imports: cli, dplyr (>= 1.1.0), ggplot2 (>= 3.5.0), igraph (>= 2.0.0),
        lgr, pROC, randomForest, ranger (>= 0.16.0), rlang, solitude
        (>= 1.1.3), stats, tibble, tidyr (>= 1.3.0), utils, withr
Suggests: knitr, plotly (>= 4.10.0), recipes, rmarkdown, smacof,
        testthat (>= 3.0.0), themis, uwot (>= 0.2.0), vdiffr
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0
NeedsCompilation: no
Packaged: 2026-06-09 14:02:19 UTC; franziska
Author: Franziska Hradilak [aut, cre]
Maintainer: Franziska Hradilak <Franziska.Hradilak@student.hpi.uni-potsdam.de>
Repository: CRAN
Date/Publication: 2026-06-17 13:20:02 UTC
