pairkat

DOI: 10.18129/B9.bioc.pairkat  

PaIRKAT

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	using-pairkat
PDF		Reference Manual
Text		NEWS

Details

biocViews	GraphAndNetwork, KEGG, Metabolomics, Network, Pathways, Regression, Software
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	SummarizedExperiment, KEGGREST, igraph, data.table, methods, stats, magrittr, CompQuadForm, tibble
LinkingTo
Suggests	rmarkdown, knitr, BiocStyle, dplyr
SystemRequirements
Enhances
URL
BugReports	https://github.com/Ghoshlab/pairkat/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	pairkat_1.4.0.tar.gz
Windows Binary	pairkat_1.4.0.zip
macOS Binary (x86_64)	pairkat_1.4.0.tgz
macOS Binary (arm64)	pairkat_1.4.0.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