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pairkat

This is the development version of pairkat; for the stable release version, see pairkat.

PaIRKAT


Bioconductor version: Development (3.19)

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.

Author: Charlie Carpenter [aut], Cameron Severn [aut], Max McGrath [cre, aut]

Maintainer: Max McGrath <max.mcgrath at ucdenver.edu>

Citation (from within R, enter citation("pairkat")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("pairkat")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("pairkat")
using-pairkat HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GraphAndNetwork, KEGG, Metabolomics, Network, Pathways, Regression, Software
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1)
Imports SummarizedExperiment, KEGGREST, igraph, data.table, methods, stats, magrittr, CompQuadForm, tibble
System Requirements
URL
Bug Reports https://github.com/Ghoshlab/pairkat/issues
See More
Suggests rmarkdown, knitr, BiocStyle, dplyr
Linking To
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package pairkat_1.9.0.tar.gz
Windows Binary pairkat_1.9.0.zip
macOS Binary (x86_64) pairkat_1.9.0.tgz
macOS Binary (arm64) pairkat_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pairkat
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pairkat
Bioc Package Browser https://code.bioconductor.org/browse/pairkat/
Package Short Url https://bioconductor.org/packages/pairkat/
Package Downloads Report Download Stats