Package: pairkat
Type: Package
Title: PaIRKAT
Version: 1.18.0
Authors@R: 
    c(person("Charlie",
             "Carpenter", 
             email = "charles.carpenter@cuanschutz.edu",
             role = c("aut")),
      person("Cameron",
             "Severn",
             email = "cameron.severn@gmail.com",
             role = c("aut")),
      person("Max",
             "McGrath",
             email = "max.mcgrath@ucdenver.edu",
             role = c("cre","aut")))
Description: PaIRKAT is model framework for assessing statistical
        relationships between networks of metabolites (pathways) and an
        outcome of interest (phenotype). PaIRKAT queries the KEGG
        database to determine interactions between metabolites from
        which network connectivity is constructed. This model framework
        improves testing power on high dimensional data by including
        graph topography in the kernel machine regression setting.
        Studies on high dimensional data can struggle to include the
        complex relationships between variables. The semi-parametric
        kernel machine regression model is a powerful tool for
        capturing these types of relationships. They provide a
        framework for testing for relationships between outcomes of
        interest and high dimensional data such as metabolomic,
        genomic, or proteomic pathways. PaIRKAT uses known biological
        connections between high dimensional variables by representing
        them as edges of ‘graphs’ or ‘networks.’ It is common for nodes
        (e.g. metabolites) to be disconnected from all others within
        the graph, which leads to meaningful decreases in testing power
        whether or not the graph information is included. We include a
        graph regularization or ‘smoothing’ approach for managing this
        issue.
License: GPL-3
Encoding: UTF-8
BugReports: https://github.com/Ghoshlab/pairkat/issues
Depends: R (>= 4.1)
Imports: SummarizedExperiment, KEGGREST, igraph, data.table, methods,
        stats, magrittr, CompQuadForm, tibble
biocViews: Software, Metabolomics, KEGG, Pathways, Network,
        GraphAndNetwork, Regression
RoxygenNote: 7.1.2
Suggests: rmarkdown, knitr, BiocStyle, dplyr
VignetteBuilder: knitr
Config/pak/sysreqs: libglpk-dev libpng-dev libxml2-dev libssl-dev
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:57:08 UTC
RemoteUrl: https://github.com/bioc/pairkat
RemoteRef: RELEASE_3_23
RemoteSha: a28d1352e49b5ac8c8a663bf4203dfd3bcb858d9
NeedsCompilation: no
Packaged: 2026-04-29 23:48:22 UTC; root
Author: Charlie Carpenter [aut],
  Cameron Severn [aut],
  Max McGrath [cre, aut]
Maintainer: Max McGrath <max.mcgrath@ucdenver.edu>
Built: R 4.6.0; ; 2026-04-30 01:21:34 UTC; unix
