attachBgrd-methods: Attach/Remove Background Intensities

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Attach/remove background intensities to/from DataTreeSet.

Usage

attachBgrd(object, treenames = "*")

removeBgrd(object)

Arguments

object	Object of class "DataTreeSet".
treenames	Object of class "list" representing the names of the ROOT background trees.

Details

Whenever one of the bgcorrect methods will be applied to raw CEL intensities, the background intensities will be stored in ROOT background trees. However, the background intensities will not be saved as data.frame bgrd, thus avoiding memory problems. Function attachBgrd allows to fill slot bgrd on demand.

attachBgrd exports intensities from background trees from ROOT data file and saves as data.frame bgrd. treenames is a vector of tree names to attach; for treenames="*" all trees from slot treenames will be exported and background intensities attached as data.frame bgrd.

removeBgrd removes background intensities from DataTreeSet and replaces data.frame bgrd with an empty data.frame of dim(0,0).

Value

A DataTreeSet object.

Note

Do not use attachBgrd unless you know that your computer has sufficient RAM, especially when using exon arrays. It may be advisible to use a subset of treenames only.

Author(s)

Christian Stratowa

See Also

attachInten, removeInten

xps documentation built on Nov. 8, 2020, 6 p.m.