Package: WSSmod 0.1.0.9000

Robert Butler

WSSmod: Weighted Sum Scores for Protein Network Modules

Computes Weighted Sum Score (WSS) module-level summaries from proteomic data. Protein-level values are sign-aligned to their association with core biomarkers and combined within 'STRING' network modules, weighted by network connectivity and association strength. Bundled reference modules and a fitted 'joinet' model also allow all module scores to be predicted from age, sex and a small panel of plasma biomarkers, without measuring the full proteomic panel. The method is described in Butler et al. (2026) <doi:10.64898/2026.08.14.26360394>.

Authors:Robert Butler [aut, cre], WSSmod authors [cph]

WSSmod_0.1.0.9000.tar.gz
WSSmod_0.1.0.9000.zip(r-4.7-any)WSSmod_0.1.0.9000.zip(r-4.6-any)WSSmod_0.1.0.9000.zip(r-4.5-any)
WSSmod_0.1.0.9000.tgz(r-4.6-any)WSSmod_0.1.0.tgz(r-4.5-any)
WSSmod_0.1.0.9000.tar.gz(r-4.7-any)WSSmod_0.1.0.9000.tar.gz(r-4.6-any)
WSSmod_0.1.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
WSSmod/json (API)

# Install 'WSSmod' in R:
install.packages('WSSmod', repos = c('https://longo-lab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/longo-lab/wssmod/issues

Pkgdown/docs site:https://longo-lab.github.io

Datasets:

On CRAN:

Conda:

5.02 score 7 scripts 15 downloads 9 exports 1 dependencies

Last updated from:6bc22b73a5. Checks:8 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK123
source / vignettesOK191
linux-releaseOK112
macos-releaseOK107
windows-develOK83
windows-releaseOK74
windows-oldrelOK71
wasm-releaseOK86

Exports:calculate_WSSlist_prebuilt_wssload_prebuilt_biomarker_referenceload_prebuilt_termsload_prebuilt_wssload_prebuilt_wss_modelnormalize_wss_biomarkerspredict_WSSproject_rank_norm

Dependencies:data.table

Exploring the bundled datasets
Available reference sets | The module and protein weighting table | Why a protein can be in several modules | Module term labels | The prediction model | The anonymized biomarker reference | Simulated example data | Provenance and use | Adding a reference set
Rendered fromexploring-datasets.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-10-21

Calculating Weighted Sum Scores
What a Weighted Sum Score is | Proteomic data and what calculate_WSS() expects | Two ways to prepare a matrix | Calculating scores with the bundled reference set | Using your own module table | Missing proteins and missing values | Scoring new samples against a reference cohort | Interpreting and comparing scores
Rendered fromcalculating-wss.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-10-20

Predicting Weighted Sum Scores from plasma biomarkers
Why predict Weighted Sum Scores | The inputs | Example data | Choosing a normalization | method = "project" (default) | method = "self" | Which to use | Predicting module scores | Reading the scores | Intended use and limits
Rendered frompredicting-wss.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-10-20