pathwayPCA

DOI: 10.18129/B9.bioc.pathwayPCA    

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Bioconductor version: Release (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>

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

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

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