biosvd: Package for high-throughput data processing, outlier detection, noise removal and dynamic modeling

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("biosvd")
AuthorAnneleen Daemen <daemena@gene.com>, Matthew Brauer <matthejb@gene.com>
Bioconductor views TimeCourse Visualization
Date of publicationNone
MaintainerAnneleen Daemen <daemena@gene.com>, Matthew Brauer <matthejb@gene.com>
LicenseArtistic-2.0
Version2.12.0

View on Bioconductor

Man pages

assayColorMap-set: Set assayColorMap for object of EigensystemPlotParam

biosvd: Package for high-throughput data processing, outlier...

compute-methods: Compute the eigensystem for a feature by assay matrix

contrast-set: Set contrast for object of EigensystemPlotParam

Eigensystem-class: The Eigensystem class

EigensystemPlotParam-class: The EigensystemPlotParam class

exclude-methods: Excludes specified eigenfeatures/eigenassays from the data

featureColorMap-set: Set featureColorMap for object of EigensystemPlotParam

figure-set: Set figure for object of EigensystemPlotParam

filenames-set: Set filenames for object of EigensystemPlotParam

HeLaData: Human HeLa Cell Cycle Expression

negativeValues-set: Set negativeValues for object of EigensystemPlotParam

palette-set: Set palette for object of EigensystemPlotParam

path-set: Set path for object of EigensystemPlotParam

plot-methods: Generate visualizations of the eigensystem

plots-set: Set plots for object of EigensystemPlotParam

prefix-set: Set prefix for object of EigensystemPlotParam

project-methods: Projects the data onto one or two eigenfeatures and...

report-methods: Creates a report of the eigensystem

StarvationData: Human HeLa Cell Cycle Expression

whichAssays-set: Set whichAssays for object of EigensystemPlotParam

whichEigenassays-set: Set whichEigenassays for object of EigensystemPlotParam

whichEigenfeatures-set: Set whichEigenfeatures for object of EigensystemPlotParam

whichFeatures-set: Set whichFeatures for object of EigensystemPlotParam

whichPolarAxes-set: Set whichPolarAxes for object of EigensystemPlotParam

YeastData: Yeast Cell Cycle Expression

Functions

apply Man page
assayColorMap Man page
assayColorMap<- Man page
assaycorrelations Man page
assayMatrix Man page
biosvd Man page
biosvd-package Man page
colorIdFeatures Man page
compute Man page
compute,data.frame-method Man page
compute,Eigensystem-method Man page
compute,ExpressionSet-method Man page
compute,matrix-method Man page
contrast Man page
contrast<- Man page
eigenassays Man page
eigenexpressions Man page
eigenfeatures Man page
Eigensystem Man page
Eigensystem-class Man page
EigensystemPlotParam Man page
EigensystemPlotParam-class Man page
entropy Man page
exclude Man page
excludeEigenfeatures Man page
exclude,Eigensystem-method Man page
featureColorMap Man page
featureColorMap<- Man page
featurecorrelations Man page
featureMatrix Man page
figure Man page
figure<- Man page
filenames Man page
filenames<- Man page
fractions Man page
HeLaData Man page
matrix Man page
negativeValues Man page
negativeValues<- Man page
palette Man page
palette<- Man page
path Man page
path<- Man page
plot Man page
plot,Eigensystem,EigensystemPlotParam-method Man page
plots Man page
plots<- Man page
prefix Man page
prefix<- Man page
project Man page
project,Eigensystem-method Man page
report Man page
report,Eigensystem,EigensystemPlotParam-method Man page
show,Eigensystem-method Man page
show,EigensystemPlotParam-method Man page
signMatrix Man page
StarvationData Man page
whichAssays Man page
whichAssays<- Man page
whichEigenassays Man page
whichEigenassays<- Man page
whichEigenfeatures Man page
whichEigenfeatures<- Man page
whichFeatures Man page
whichFeatures<- Man page
whichPolarAxes Man page
whichPolarAxes<- Man page
YeastData Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.