pathwayPCA

DOI: 10.18129/B9.bioc.pathwayPCA    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see pathwayPCA.

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Bioconductor version: 3.9

Apply the Supervised PCA and Adaptive, Elastic-Net, Sparse PCA methods to extract principal components from each pathway. Use these pathway- specific principal components as the design matrix relating the response to each pathway. Return the model fit statistic p-values, and adjust these values for False Discovery Rate. Return a data frame of the pathways sorted by their adjusted p-values. This package has corresponding vignettes hosted in the ''User Guides'' page of , and the website for the development information is hosted at .

Author: Gabriel Odom [aut, cre], James Ban [aut], Lizhong Liu [aut], Lily Wang [aut], Steven Chen [aut]

Maintainer: Gabriel Odom <gabriel.odom at med.miami.edu>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("pathwayPCA")

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("pathwayPCA")

 

HTML	R Script	Create Data Objects
HTML	R Script	Importing Data
HTML	R Script	Introduction
HTML	R Script	Quickstart Guide
HTML	R Script	Test Pathway Significance
HTML	R Script	Visualizing the Results
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBiology, Classification, CopyNumberVariation, DNAMethylation, DimensionReduction, Epigenetics, FeatureExtraction, FunctionalGenomics, GeneExpression, GenePrediction, GeneSetEnrichment, GeneSignaling, GeneTarget, Genetics, GenomeWideAssociation, GenomicVariation, Lipidomics, Metabolomics, MultipleComparison, Pathways, PrincipalComponent, Proteomics, Regression, SNP, Software, Survival, SystemsBiology, Transcription, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
License	GPL-3
Depends	R (>= 3.6)
Imports	lars, methods, parallel, stats, survival, utils
LinkingTo
Suggests	airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse
SystemRequirements
Enhances
URL	https://gabrielodom.github.io/pathwayPCA/; https://github.com/gabrielodom/pathwayPCA
BugReports	https://github.com/gabrielodom/pathwayPCA/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	pathwayPCA_1.0.0.tar.gz
Windows Binary	pathwayPCA_1.0.0.zip
Mac OS X 10.11 (El Capitan)	pathwayPCA_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pathwayPCA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pathwayPCA
Package Short Url	https://bioconductor.org/packages/pathwayPCA/
Package Downloads Report	Download Stats