pcaMethods

A collection of PCA methods.

Bioconductor version: 2.8

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 unique interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany. Now developed at CAS-MPG Partner Institute for Computational Biology (PICB) Shanghai, P.R. China and RIKEN Plant Science Center, Yokohama Japan.

Author: Wolfram Stacklies, Henning Redestig, Kevin Wright

Maintainer: Wolfram Stacklies <wolfram.stacklies 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

Details

biocViews Bioinformatics
Depends Biobase, MASS, pls, methods, Rcpp (>= 0.8.7)
Imports
Suggests aroma.light
System Requirements Rcpp
License GPL (>= 3)
URL
Depends On Me
Imports Me
Suggests Me
Version 1.36.0
Since Bioconductor 1.9 (R-2.4)

Package Downloads

Package Source pcaMethods_1.36.0.tar.gz
Windows Binary pcaMethods_1.36.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary pcaMethods_1.36.0.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:

 

Mailing Lists »

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

Fred Hutchinson Cancer Research Center