Package: pairkat
Type: Package
Title: PaIRKAT
Version: 1.9.0
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