DOI: 10.18129/B9.bioc.pcaMethods    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see pcaMethods.

A collection of PCA methods

Bioconductor version: 3.8

Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany.

Author: Wolfram Stacklies, Henning Redestig, Kevin Wright

Maintainer: Henning Redestig <henning.red at gmail.com>

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PDF R Script Data with outliers
PDF R Script Introduction
PDF R Script Missing value imputation
PDF   Reference Manual


biocViews Bayesian, Software
Version 1.74.0
In Bioconductor since BioC 1.9 (R-2.4) (12.5 years)
License GPL (>= 3)
Depends Biobase, methods
Imports BiocGenerics, Rcpp (>= 0.11.3), MASS
LinkingTo Rcpp
Suggests matrixStats, lattice, ggplot2
SystemRequirements Rcpp
URL https://github.com/hredestig/pcamethods
BugReports https://github.com/hredestig/pcamethods/issues
Depends On Me DeconRNASeq
Imports Me CompGO, consensusDE, DAPAR, MSnbase, OUTRIDER, PanVizGenerator, scde, SomaticSignatures
Suggests Me mtbls2
Links To Me
Build Report  

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Source Package pcaMethods_1.74.0.tar.gz
Windows Binary pcaMethods_1.74.0.zip
Mac OS X 10.11 (El Capitan) pcaMethods_1.74.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pcaMethods
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pcaMethods
Package Short Url http://bioconductor.org/packages/pcaMethods/
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