pairkat

DOI: 10.18129/B9.bioc.pairkat    

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

PaIRKAT

Bioconductor version: Development (3.15)

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 [cre, aut]

Maintainer: Cameron Severn <cameron.severn at gmail.com>

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

Installation

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

if (!requireNamespace("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")

 

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Details

biocViews GraphAndNetwork, KEGG, Metabolomics, Network, Pathways, Regression, Software
Version 1.1.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
License GPL-3
Depends R (>= 4.1), KEGGREST, S4Vectors, SummarizedExperiment, igraph, data.table, methods, stats
Imports dplyr, magrittr, CompQuadForm, tibble
LinkingTo
Suggests rmarkdown, knitr, BiocStyle
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_1.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) pairkat_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pairkat
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pairkat
Package Short Url https://bioconductor.org/packages/pairkat/
Package Downloads Report Download Stats

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