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 (may not be active yet) |
| 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 |