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
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("pathwayPCA")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| 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 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
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) (5 years) |
| License | GPL-3 |
| Depends | R (>= 3.6) |
| Imports | lars, methods, parallel, stats, survival, utils |
| System Requirements | |
| URL | https://gabrielodom.github.io/pathwayPCA/; https://github.com/gabrielodom/pathwayPCA |
| Bug Reports | https://github.com/gabrielodom/pathwayPCA/issues |
See More
| Suggests | airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/pathwayPCA/ |
| Package Short Url | https://bioconductor.org/packages/pathwayPCA/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |