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

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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.

Author
Anneleen Daemen <daemena@gene.com>, Matthew Brauer <matthejb@gene.com>
Date of publication
None
Maintainer
Anneleen Daemen <daemena@gene.com>, Matthew Brauer <matthejb@gene.com>
License
Artistic-2.0
Version
2.10.0

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

Files in this package

biosvd/DESCRIPTION
biosvd/HeLaData.eigenexpressionFraction.pdf
biosvd/HeLaData.eigenfeatureLevelXassays.selected.pdf
biosvd/HeLaData.eigenfeatureXassay.heatmap.pdf
biosvd/NAMESPACE
biosvd/R
biosvd/R/AllClasses.R
biosvd/R/AllGenerics.R
biosvd/R/biosvd-package.R
biosvd/R/methods-Eigensystem-class.R
biosvd/R/methods-EigensystemPlotParam-class.R
biosvd/R/methods-compute.R
biosvd/R/methods-exclude.R
biosvd/R/methods-plot.R
biosvd/R/methods-project.R
biosvd/R/methods-report.R
biosvd/build
biosvd/build/vignette.rds
biosvd/data
biosvd/data/HeLaData_exp_DoubleThym_2.RData
biosvd/data/StarvationData.RData
biosvd/data/YeastData_alpha.RData
biosvd/inst
biosvd/inst/NEWS
biosvd/inst/doc
biosvd/inst/doc/biosvd.R
biosvd/inst/doc/biosvd.Rnw
biosvd/inst/doc/biosvd.pdf
biosvd/man
biosvd/man/Eigensystem-class.Rd
biosvd/man/EigensystemPlotParam-class.Rd
biosvd/man/HeLaData.Rd
biosvd/man/StarvationData.Rd
biosvd/man/YeastData.Rd
biosvd/man/assayColorMap-set.Rd
biosvd/man/biosvd.Rd
biosvd/man/compute-methods.Rd
biosvd/man/contrast-set.Rd
biosvd/man/exclude-methods.Rd
biosvd/man/featureColorMap-set.Rd
biosvd/man/figure-set.Rd
biosvd/man/filenames-set.Rd
biosvd/man/negativeValues-set.Rd
biosvd/man/palette-set.Rd
biosvd/man/path-set.Rd
biosvd/man/plot-methods.Rd
biosvd/man/plots-set.Rd
biosvd/man/prefix-set.Rd
biosvd/man/project-methods.Rd
biosvd/man/report-methods.Rd
biosvd/man/whichAssays-set.Rd
biosvd/man/whichEigenassays-set.Rd
biosvd/man/whichEigenfeatures-set.Rd
biosvd/man/whichFeatures-set.Rd
biosvd/man/whichPolarAxes-set.Rd
biosvd/vignettes
biosvd/vignettes/biosvd-package-overview.png
biosvd/vignettes/biosvd.Rnw