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.
| Version: | 0.1.0 |
| 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 |
| Published: | 2026-06-17 |
| DOI: | 10.32614/CRAN.package.spqrp |
| Author: | Franziska Hradilak [aut, cre] |
| Maintainer: | Franziska Hradilak <Franziska.Hradilak at student.hpi.uni-potsdam.de> |
| BugReports: | https://github.com/fhradilak/spqrp_r/issues |
| License: | GPL-3 |
| URL: | https://github.com/fhradilak/spqrp_r |
| NeedsCompilation: | no |
| Citation: | spqrp citation info |
| Materials: | README, NEWS |
| CRAN checks: | spqrp results |
| Reference manual: | spqrp.html , spqrp.pdf |
| Vignettes: |
spqrp on mock data (source, R code) |
| Package source: | spqrp_0.1.0.tar.gz |
| Windows binaries: | r-devel: spqrp_0.1.0.zip, r-release: spqrp_0.1.0.zip, r-oldrel: spqrp_0.1.0.zip |
| macOS binaries: | r-release (arm64): spqrp_0.1.0.tgz, r-oldrel (arm64): spqrp_0.1.0.tgz, r-release (x86_64): spqrp_0.1.0.tgz, r-oldrel (x86_64): spqrp_0.1.0.tgz |
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