Package: biosvd
Type: Package
Title: Package for high-throughput data processing, outlier detection,
        noise removal and dynamic modeling
Version: 1.0.0
Date: 2013-12-11
Author: Anneleen Daemen <daemena@gene.com>, Matthew Brauer
        <matthejb@gene.com>
Maintainer: Anneleen Daemen <daemena@gene.com>, Matthew Brauer
 <matthejb@gene.com>
Description: The biosvd package contains functions to reduce the input
        data set from the feature x assay space to the reduced
        diagonalized eigenfeature x eigenassay space, with the
        eigenfeatures and eigenassays unique orthonormal superpositions
        of the features and assays, respectively. Results of SVD
        applied to the data can subsequently be inspected based on
        generated graphs, such as a heatmap of the eigenfeature x assay
        matrix and a bar plot with the eigenexpression fractions of all
        eigenfeatures. These graphs aid in deciding which eigenfeatures
        and eigenassays to filter out (i.e., eigenfeatures representing
        steady state, noise, or experimental artifacts; or when applied
        to the variance in the data, eigenfeatures representing
        steady-scale variance). After possible removal of steady state
        expression, steady-scale variance, noise and experimental
        artifacts, and after re-applying SVD to the normalized data, a
        summary html report of the eigensystem is generated, containing
        among others polar plots of the assays and features, a table
        with the list of features sortable according to their
        coordinates, radius and phase in the polar plot, and a
        visualization of the data sorted according to the two selected
        eigenfeatures and eigenassays with colored feature/assay
        annotation information when provided. This gives a global
        picture of the dynamics of expression/intensity levels, in
        which individual features and assays are classified in groups
        of similar regulation and function or similar cellular state
        and biological phenotype.
License: Artistic-2.0
Depends: R (>= 3.0.0)
Imports: gplots, BiocGenerics, Biobase, methods, grid, hwriter,
        ReportingTools, graphics
biocViews: TimeCourse, Visualization
Packaged: 2014-04-12 10:39:59 UTC; biocbuild
Built: R 3.1.0; ; 2014-04-12 11:47:05 UTC; windows
