attachInten-methods: Attach/Remove Intensities

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

Description

Attach/remove raw CEL intensities to/from DataTreeSet.

Usage

attachInten(object, treenames = "*")

removeInten(object)

Arguments

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

Details

When CEL files will be imported using function import.data, the raw intensities will be stored in ROOT data trees. However, the intensities will not be saved in class DataTreeSet as slot data, thus avoiding memory problems. Function attachInten allows to fill slot data on demand.

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

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

Value

A DataTreeSet object.

Note

Do not use attachInten 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

attachBgrd, removeBgrd

Examples

## load existing ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))
dim(intensity(data.test3))

data.test3 <- attachInten(data.test3)
dim(intensity(data.test3))
head(intensity(data.test3))

data.test3 <- removeInten(data.test3)
dim(intensity(data.test3))

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