report-methods: Creates a report of the eigensystem

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

Description

Generates a summarizing report of the eigensystem

Usage

## S4 method for signature 'Eigensystem,EigensystemPlotParam'
report(x, y, ...)

Arguments

x	object of class Eigensystem
y	object of class EigensystemPlotParam
...	Additional arguments that can be passed on

Details

The function generates a txt file of the eigensystem, containing the list of features with their coordinates, radius and phase in the polar plot according to two selected eigenfeatures.

Methods

signature(x = "Eigensystem", y = "EigensystemPlotParam")

Author(s)

Anneleen Daemen [e-mail], Matthew Brauer [e-mail]

See Also

Other X.eigensystem.: compute, compute,Eigensystem-method, compute,ExpressionSet-method, compute,data.frame-method, compute,matrix-method; exclude, exclude,Eigensystem-method; plot, plot,Eigensystem,EigensystemPlotParam-method

Examples

## Metabolomics starvation data obtained from http://genomics-pubs.princeton.edu/StarvationMetabolomics/Download.shtml
data(StarvationData)

## Computes the eigensystem for the actual data
eigensystem <- compute(StarvationData)
## Exclude the eigenfeatures representing steady-state intensity
eigensystem <- exclude(eigensystem)
## Computes the eigensystem on the variance in the data after filtering out stead-state intensity
eigensystem <- compute(eigensystem, apply="variance")
## No exclusion of eigenfeatures representing steady-scale variance
eigensystem <- exclude(eigensystem, excludeEigenfeatures=0)

## Generate report for eigenfeatures 1 and 2
params <- new("EigensystemPlotParam")
if (.Platform$OS.type %in% "windows") path(params) <- getwd()
report(eigensystem, params)
## Generate report for eigenfeatures 2 and 3
whichPolarAxes(params) <- c(3,2)
report(eigensystem, params)

biosvd documentation built on April 28, 2020, 6:32 p.m.