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.

AuthorAnneleen Daemen <daemena@gene.com>, Matthew Brauer <matthejb@gene.com>
Date of publicationNone
MaintainerAnneleen Daemen <daemena@gene.com>, Matthew Brauer <matthejb@gene.com>
LicenseArtistic-2.0
Version2.10.0

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

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