attachUnitNames-methods: Attach/Remove Unit Names

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

Description

Attach/remove unit names, i.e. the Affymetrix probeset IDs to/from SchemeTreeSet or to slot scheme of DataTreeSet.

Usage

attachUnitNames(object, treetype = "idx")

removeUnitNames(object)

Arguments

object	Object of class "SchemeTreeSet" or "DataTreeSet".
treetype	the unit tree type, i.e. ‘idx’ or ‘pbs’.

Details

attachUnitNames exports “UnitName” from unit tree of ROOT scheme file and and saves it as data.frame in slot unitname.

removeUnitNames removes unitname from slot unitname and replaces data.frame unitname with an empty data.frame of dim(0,0).

For treetype="idx" the internal “UNIT_ID” will be mapped to the Affymetrix probeset IDs of the expression arrays or to the transcript_cluster_ids of the exon arrays, respectively, as “UnitName”.

For treetype="pbs" the internal “UNIT_ID” will be mapped to the Affymetrix probeset_ids of the exon arrays as “UnitName”.

Value

A DataTreeSet object or SchemeTreeSet.

Note

Do not use attachUnitNames unless you know that your computer has sufficient RAM, especially for exon array schemes.

Author(s)

Christian Stratowa

See Also

attachMask, removeMask

Examples

## first, load ROOT scheme file
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))

## attach unitname
scheme.test3 <- attachUnitNames(scheme.test3)

## get data.frame
unitnames <- unitNames(scheme.test3)
head(unitnames)

## remove unitname
scheme.test3 <- removeUnitNames(scheme.test3)

rm(scheme.test3)
gc()

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