pcaMethods

A collection of PCA methods.

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("pcaMethods")

To cite this package in a publication, start R and enter:

    citation("pcaMethods")

Documentation

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

Details

biocViews Bayesian, Software
Version 1.55.0
In Bioconductor since BioC 1.9 (R-2.4)
License GPL (>= 3)
Depends Biobase, methods, Rcpp (>= 0.8.7)
Imports BiocGenerics, MASS
Suggests matrixStats, lattice
System Requirements Rcpp
URL
Depends On Me DeconRNASeq
Imports Me MSnbase, SomaticSignatures
Suggests Me

Package Downloads

Package Source pcaMethods_1.55.0.tar.gz
Windows Binary pcaMethods_1.55.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) pcaMethods_1.55.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center